I couldn't find a comprehensive list of all US Zelda game variants, so I made one. I'm sure I'm missing a couple obscure things, so please post any that are missing. Some of the variant descriptions are a bit terse, so if any are confusing just ask.

Rules:

• Must be a US version
• Must include a game (I also included console bundles with digital games)
• To be a seperate variant the cartridge/disc, box, or manual cover must be different in some way (I don't want to go down the rabbit hole of other inserts or minor manual changes)
• No prototypes or factory errors (another rabbit hole)

The List:

Platform	Title
NES	Legend of Zelda [5 Screw, TM]
NES	Legend of Zelda [5 Screw, R]
NES	Legend of Zelda [Circle SOQ, No Made in Japan]
NES	Legend of Zelda [Circle SOQ, No Code, Old Image]
NES	Legend of Zelda [Circle SOQ, No Code, New Image]
NES	Legend of Zelda [Circle SOQ, No Code, Rev-A, All Black Text]
NES	Legend of Zelda [Circle SOQ, No Code, Rev-A, Red Text]
NES	Legend of Zelda [Circle SOQ, No Code, Game-Pak]
NES	Legend of Zelda [Circle SOQ, Code]
NES	Legend of Zelda [Circle SOQ, Code, 85 on Cart Back]
NES	Legend of Zelda [Oval SOQ TM]
NES	Legend of Zelda [Oval SOQ TM, ZIP+4]
NES	Legend of Zelda [Oval SOQ R]
NES	Legend of Zelda [Classic Series]
NES	Legend of Zelda [Test Cartridge, 3 Screw]
NES	Legend of Zelda [Test Cartridge, 5 Screw]
NES	Legend of Zelda [NFR]
NES	Zelda II: The Adventure of Link [Circle SOQ]
NES	Zelda II: The Adventure of Link [Circle SOQ, 85 on Cart Back]
NES	Zelda II: The Adventure of Link [Oval SOQ TM]
NES	Zelda II: The Adventure of Link [Oval SOQ TM, ZIP+4]
NES	Zelda II: The Adventure of Link [Oval SOQ R]
NES	Zelda II: The Adventure of Link [Classic Series]
NES	Zelda II: The Adventure of Link [NFR]
Watch	The Legend of Zelda Game Watch [Black]
Watch	The Legend of Zelda Game Watch [Red]
Watch	The Legend of Zelda Game Watch [Pink]
Watch	The Legend of Zelda Game Watch [White]
Watch	The Legend of Zelda Game Watch [Black Blister Pack]
Game & Watch	Zelda [ZL-65]
Mini Classics	Zelda [1998 Release]
Mini Classics	Zelda [2007 Release]
SNES	Legend of Zelda: A Link To The Past
SNES	Legend of Zelda: A Link To The Past [-1 Manual]
SNES	Legend of Zelda: A Link To The Past [-2 Manual]
SNES	Legend of Zelda: A Link To The Past [Player's Choice, Made in Mexico]
SNES	Legend of Zelda: A Link To The Past [Player's Choice, K-A Rating]
SNES	Legend of Zelda: A Link To The Past [Player's Choice, E Rating]
SNES	Legend of Zelda: A Link To The Past [Control Set Bundle, SNS-S-HA-USA, Free!]
SNES	Legend of Zelda: A Link To The Past [Control Set Bundle, SNS-S-HA-USA, Special Offer!]
SNES	Legend of Zelda: A Link To The Past [Control Set Bundle, SNS-S-HA-USA-1]
SNES	Legend of Zelda: A Link To The Past [Control Deck Bundle]
SNES	Legend of Zelda: A Link To The Past [NFR]
Game Boy	Legend of Zelda: Link's Awakening
Game Boy	Legend of Zelda: Link's Awakening [Player's Choice, K-A Rating, -0 Manual]
Game Boy	Legend of Zelda: Link's Awakening [Player's Choice, K-A Rating, -1 Manual]
Game Boy	Legend of Zelda: Link's Awakening [E Rating]
Game Boy	Legend of Zelda: Link's Awakening [Player's Choice, E Rating]
Game Boy	Legend of Zelda: Link's Awakening [Original Game Boy Bundle]
Game Boy	Legend of Zelda: Link's Awakening [Ice Blue Pocket Bundle]
Game Boy	Legend of Zelda: Link's Awakening [NFR, cart sticker]
Game Boy	Legend of Zelda: Link's Awakening [NFR, box sticker]
CD-i	Zelda: The Wand of Gamelon
CD-i	Zelda: The Wand of Gamelon [NFR]
CD-i	Link: The Faces of Evil
CD-i	Link: The Faces of Evil [NFR]
CD-i	Zelda's Adventure
CD-i	Zelda's Adventure [NFR]
N64	Legend of Zelda: Ocarina of Time
N64	Legend of Zelda: Ocarina of Time [Collector's Edition]
N64	Legend of Zelda: Ocarina of Time [Player's Choice]
N64	Legend of Zelda: Ocarina of Time [NFR Gold]
N64	Legend of Zelda: Ocarina of Time [NFR Gray]
N64	Legend of Zelda: Majora's Mask
N64	Legend of Zelda: Majora's Mask [-1 Manual]
N64	Legend of Zelda: Majora's Mask [Collector's Edition]
N64	Legend of Zelda: Majora's Mask [Collector's Edition, -1 Manual]
N64	Legend of Zelda: Majora's Mask [NFR Gold]
N64	Legend of Zelda: Majora's Mask [NFR Gray]
GBC	Legend of Zelda: Link's Awakening DX
GBC	Legend of Zelda: Link's Awakening DX [U/ Box and Manual]
GBC	Legend of Zelda: Link's Awakening DX [SOQ]
GBC	Legend of Zelda: Link's Awakening DX [NFR]
GBC	Legend of Zelda: Oracle of Ages [Metallic "Only For"]
GBC	Legend of Zelda: Oracle of Ages [Gray "Only For"]
GBC	Legend of Zelda: Oracle of Ages [NFR]
GBC	Legend of Zelda: Oracle of Seasons [Metallic "Only For"]
GBC	Legend of Zelda: Oracle of Seasons [Gray "Only For"]
GBC	Legend of Zelda: Oracle of Seasons [NFR]
GBA	Legend of Zelda: A Link To The Past and Four Swords [100% Recovered Fiber]
GBA	Legend of Zelda: A Link To The Past and Four Swords [83% Recovered Fiber]
GBA	Legend of Zelda: A Link To The Past and Four Swords [Player's Choice Box]
GBA	Legend of Zelda: A Link To The Past and Four Swords [NFR]
GBA	The Legend of Zelda [Classic NES Series]
GBA	The Legend of Zelda [Classic NES Series, -1 Manual]
GBA	The Legend of Zelda [Classic NES Series, Red SP Bundle]
GBA	Zelda II: The Adventure of Link [Classic NES Series]
GBA	Zelda II: The Adventure of Link [Classic NES Series, Red SP Bundle]
GBA	Zelda II: The Adventure of Link [Classic NES Series, Silver SP Bundle]
GBA	The Legend of Zelda: The Minish Cap
GBA	The Legend of Zelda: The Minish Cap [NFR]
GBA	The Legend of Zelda: The Minish Cap [NFR Demo]
Gamecube	Legend of Zelda: The Wind Waker [UPC 5: 00000]
Gamecube	Legend of Zelda: The Wind Waker [UPC 5: 00100]
Gamecube	Legend of Zelda: The Wind Waker [Player's Choice, UPC 5: 00001]
Gamecube	Legend of Zelda: The Wind Waker [Player's Choice, UPC 5: 00100]
Gamecube	Legend of Zelda: The Wind Waker [Player's Choice, UPC 5: 00101]
Gamecube	Legend of Zelda: The Wind Waker [For Rental Use]
Gamecube	Legend of Zelda: The Wind Waker [K-Mart]
Gamecube	Legend of Zelda: The Wind Waker [Platinum Gamecube Bundle]
Gamecube	Legend of Zelda: Wind Waker & Metroid Prime [Platinum Gamecube Bundle]
Gamecube	Legend of Zelda: Wind Waker & Ocarina of Time Master Quest [Indigo Gamecube Bundle]
Gamecube	Legend of Zelda: Ocarina of Time [Master Quest]
Gamecube	Legend of Zelda: Ocarina of Time [Master Quest/Game Boy Player, Platinum Bundle]
Gamecube	Legend of Zelda: Collector's Edition [UPC 5: 00000]
Gamecube	Legend of Zelda: Collector's Edition [UPC 5: 00100]
Gamecube	Legend of Zelda: Collector's Edition [Black Gamecube Bundle, GB-DOL-S-KB-USA-2]
Gamecube	Legend of Zelda: Collector's Edition [Black Gamecube Bundle, C/GB-DOL-S-KB-USA-1]
Gamecube	Legend of Zelda: Collector's Edition [Black Gamecube Bundle & Carrying Case, GB-DOL-S-KB-USA-2]
Gamecube	Legend of Zelda: Collector's Edition [Black Gamecube Bundle & Carrying Case, C/GB-DOL-S-KB-USA-1]
Gamecube	Legend of Zelda: Collector's Edition [Indigo Gamecube Bundle]
Gamecube	Legend of Zelda: Collector's Edition [Platinum Gamecube Bundle]
Gamecube	Legend of Zelda: Four Swords Adventures
Gamecube	Legend of Zelda: Four Swords Adventures [Player's Choice]
Gamecube	Legend of Zelda: Four Swords Adventures [Big Box]
Gamecube	Legend of Zelda: Twilight Princess
Wii	Legend of Zelda: Twilight Princess [UPC 5: 00000]
Wii	Legend of Zelda: Twilight Princess [UPC 5: 00100, Ver 1.0]
Wii	Legend of Zelda: Twilight Princess [UPC 5: 00100, Ver 1.2]
Wii	Legend of Zelda: Twilight Princess [UPC 5: 00101]
Wii	Legend of Zelda: Twilight Princess [UPC 5: 00102]
Wii	Legend of Zelda: Twilight Princess [Nintendo Selects]
Wii	Legend of Zelda: Twilight Princess [NFR]
Wii	Link’s Crossbow Training [Blue Box Sides]
Wii	Link’s Crossbow Training [White Box Sides]
Wii	Legend of Zelda: Skyward Sword
Wii	Legend of Zelda: Skyward Sword [Music CD Bundle]
Wii	Legend of Zelda: Skyward Sword [Sword Bundle]
Wii	Legend of Zelda: Skyward Sword [NFR]
DS	Legend of Zelda: Twilight Princess Demo [NFR]
DS	Legend of Zelda: Phantom Hourglass
DS	Legend of Zelda: Phantom Hourglass [DS Lite Bundle]
DS	Legend of Zelda: Phantom Hourglass [NFR]
DS	Legend of Zelda: Spirit Tracks
DS	Legend of Zelda: Spirit Tracks [NFR]
3DS	Legend of Zelda: Ocarina of Time 3D [UPC 5: 00000]
3DS	Legend of Zelda: Ocarina of Time 3D [UPC 5: 00001]
3DS	Legend of Zelda: Ocarina of Time 3D [Nintendo Selects]
3DS	Legend of Zelda: Ocarina of Time 3D [3DS Bundle]
3DS	Legend of Zelda: Ocarina of Time 3D [2DS Bundle]
3DS	Legend of Zelda: Ocarina of Time 3D [NFR]
3DS	The Legend of Zelda: A Link Between Worlds
3DS	The Legend of Zelda: A Link Between Worlds [Game of the Year]
3DS	The Legend of Zelda: A Link Between Worlds [Nintendo Selects, UPC 5: 00000]
3DS	The Legend of Zelda: A Link Between Worlds [Nintendo Selects, UPC 5: 00001]
3DS	The Legend of Zelda: A Link Between Worlds [3DS XL Bundle]
3DS	The Legend of Zelda: A Link Between Worlds [New 2DS XL Hylian Shield Edition]
3DS	The Legend of Zelda: A Link Between Worlds [NFR]
3DS	Legend of Zelda: Majora's Mask 3D
3DS	Legend of Zelda: Majora's Mask 3D [Nintendo Selects]
3DS	Legend of Zelda: Majora's Mask 3D [Limited Edition]
3DS	Legend of Zelda: Majora's Mask 3D [NFR]
3DS	Legend of Zelda: Tri Force Heroes
3DS	Hyrule Warriors Legends
3DS	Hyrule Warriors Legends [NFR]
Wii U	Legend of Zelda: The Wind Waker HD
Wii U	Legend of Zelda: The Wind Waker HD [Blue Globe]
Wii U	Legend of Zelda: The Wind Waker HD [Nitendo Selects]
Wii U	Legend of Zelda: The Wind Waker HD [Limited Edition]
Wii U	Legend of Zelda: The Wind Waker HD [Wii U Bundle]
Wii U	Hyrule Warriors [UPC 5: 00100]
Wii U	Hyrule Warriors [UPC 5: 00101]
Wii U	Hyrule Warriors [Limited Edition]
Wii U	Legend of Zelda: Twilight Princess HD
Wii U	Legend of Zelda: Twilight Princess HD [Amiibo Bundle]
Wii U	The Legend of Zelda: Breath of the Wild [UPC 5: 00000]
Wii U	The Legend of Zelda: Breath of the Wild [UPC 5: 00001]
Switch	The Legend of Zelda: Breath of the Wild [UPC 5: 00000]
Switch	The Legend of Zelda: Breath of the Wild [UPC 5: 00001]
Switch	The Legend of Zelda: Breath of the Wild [Special Edition]
Switch	The Legend of Zelda: Breath of the Wild [Master Edition]
Switch	The Legend of Zelda: Breath of the Wild [Explorer's Edition]
Switch	The Legend of Zelda: Breath of the Wild [Starter Pack]
Switch	Hyrule Warriors: Definitive Edition
Switch	The Legend of Zelda: Link's Awakening
Switch	The Legend of Zelda: Link's Awakening [Dreamer's Edition]

Honarable mentions go to "New 3DS XL: Hyrule Edition" and "New 3DS XL: Majora's Mask Edition" which were the only two zelda consoles I found that didn't include a game.

---

While doing the research for this, I came across several things I couldn't confirm, so following are the things I still have questions about.

For most manual revisions after SNES, I am not sure which cart or box revision they match up with. Therefore, it's likely that there are more variants where only the manual changed.

For both Link's Awakening and Link's Awakening DX, I found high revision manuals (-4 and -2 respectively) without find some in between. The ones I'm missing are DMG-ZL-USA-2, DMG-ZL-USA-3, and DMG-AZLE-USA-1. It's worth noting that DMG-ZL-USA-4 came with the ice blue pocket bundle.

I found a couple of far away shots for Ocarina Of Time 3D that look different from every version I can find.
One is is at the top left (below the Skyward Sword bundle) of the second photo here http://nintendoage.com/forum/messageview.cfm?catid=5&thr...
The other at the top right of the Ocarina Of Time 3D group photo here http://nintendoage.com/forum/messageview.cfm?catid=5&thr...
The first has a black triangle in the lower left that I guess might be a retailer promo. The second has two rows of text at the bottom.

There is a yellow box art for Wind Waker (https://gamepedia.cursecdn.com/zelda_gamepedia_en/thumb/b/b7... ). I tried to do some research and found a couple of suggestions that it might be the pre order version (or first couple months of release) of the game. However, after going through > 1.5k pictures on ebay, I've yet to come across a single physical version with this box art. I'm guessing it was only used for promotional purposes, but it would be nice if someone could confirm.

It seems like some Wii and WiiU games received refurbished variants (see here http://nintendoage.com/forum/messageview.cfm?catid=5&thr... ). Does anyone know if there were any zelda refurbished variants?

According to JaxsBox there is an E3 variant for A Link Between Worlds [NFR] (http://nintendoage.com/forum/messageview.cfm?catid=5&thr... ). There is a picture but it is too small to see what the differences are between the E3 NFR and the regular NFR.

Well, this is amazing, thank you! Gonna check to see what 5-screw variant I own when I get home. haha  

I'm not sure about any zelda refurbs. If there were, they'd probably be really rare if not even rarer than the other ones Nintendo pumped out. If I hear anything, I'll let you know.

Somehow when I was messing around with formatting it deleted half the table, so I've fixed it. I found out that there were multiple colors for the nelsonic watches as well as a blister pack version, added those. When going through my research again, I saw another gamecube bundle again I thought I already had. Ordered the table better to be closer to release order (while still grouping by console then base game). Also I forgot to mention in the rule that I'm ignoring prototypes and factory errors as they're another rabbit hole I don't want to go down. The most popular variant list for the NES zeldas is Braveheart's (http://nintendoage.com/forum/messageview.cfm?catid=5&thr... ), but around post 69 mb7241 discovered that there is another 5 screw variant with the ®. Checking ebay confirms this. It doesn't even seem that much rarer than the TM one.

While I'm talking about this, I should probably share some resources I used for more information.

General: https://zelda.gamepedia.com was helpful for all the main games, several spin-offs, and especially their box art gallery which helped with limited editions. https://nfr.fandom.com helped for all things kiosk NFR. https://zeldacollection.com had a lot of random obscure stuff. It also has a bunch or stuff for other regions which wasn't needed for this list, but interesting nonetheless. A nice list of US console bundles are here http://nintendoage.com/forum/messageview.cfm?catid=5&thr... .

NES: The Legend of Zelda stuff is above. Braveheart's Zelda II list is here http://nintendoage.com/forum/messageview.cfm?catid=5&thr... . Test cart screw variants http://nintendoage.com/forum/messageview.cfm?StartRow=1&... . The NFRs also say Nintendo Promotional Offer and seem to come from an NOA library. Picture of both here http://web.archive.org/web/20090725071306/http://zeldacollec... . More information on where they came from is here http://nintendoage.com/forum/messageview.cfm?catid=10&th... .

LCD: Tons of information can be found at https://zelda.gamepedia.com/Zelda_(Game_%26_Watch) and https://zelda.gamepedia.com/The_Legend_of_Zelda_Game_Watch. 

SNES: Cart, box, and manual information is given here https://snescentral.com/article.php?id=0164. I was able to piece together likely pairings by going through ebay pictures. The NFR uses a different stick but the purpose seems the same as the NES NFRs. Info here http://nintendoage.com/forum/messageview.cfm?catid=8&thr... .

Game Boy: Cart variants documented here http://nintendoage.com/forum/messageview.cfm?catid=5&thr... . The ice blue pocket bundle had a rectangular manual. More on that here http://nintendoage.com/forum/messageview.cfm?catid=5&thr... . NFR box sticker is the same as aLttP, but here's another thread for it http://nintendoage.com/forum/messageview.cfm?catid=29&th... .

N64: Nothing crazy here. Notable NFRs: MM gray is a demo and very rare, OoT gold is back sticker only. Majora's Mask also had a manual revision due to an accidental reference to a nonexistant 4-player mode.

GBC: Link's Awakening DX info http://nintendoage.com/forum/messageview.cfm?catid=5&thr... . I discovered that OoA had two printings here https://zeldacollection.com/game-boy-color/the-legend-of-zel... . I checked ebay and sure enough OoS has the same two printings.

GBA: Again, I found out about the two printings of the original version of Four Swords here https://zeldacollection.com/game-boy-advance/the-legend-of-z... . It discribes that the first printing has a sold metaliic left side whereas the second printing has a slight gradient to white. It can sometimes be hard to tell with bad photography, so another way is to look under the recycle sign where the text is X% total recovered fiber. X can be 100 or 83. Pictures of three SP bundles are here as well as the two Game Boy bundles http://nintendoage.com/forum/messageview.cfm?.StartRow=1&... .

Gamecube: A nice list of game variants can be found here http://nintendoage.com/forum/messageview.cfm?catid=8&thr... . It doesn't cover any console bundles though. Three WW games (PC NFR, Metroid Combo, Master Quest Combo) were only available through console bundles. Regular Master Quest and Collector's Edition were both avaiable as standalone and in bundles. A lot of these bundles I was able to confirm with pictures from https://www.instagram.com/joaquin.zeldacollector/. More info about the WW + Metroid bundle is here https://forum.digitpress.com/forum/showthread.php?161233-Bes...  and here http://nintendoage.com/forum/messageview.cfm?catid=5&thr... .

Wii: Nothing special here.

DS: Or here, the Lite bundle is from the console bundle resource in general.

3DS: Console bundles found here https://en.wikipedia.org/wiki/List_of_Nintendo_3DS_colors_an... . Game of the Year found here https://zeldacollection.com/nintendo-3ds/the-legend-of-zelda... .

Wii U: I learned that the blue globe was a variant here https://zeldacollection.com/nintendo-wii-u/the-legend-of-zel... .

Switch: Most of these limited editions and many previous ones were gathered from this https://zelda.gamepedia.com/Gallery:Box_Art.

This is awesome.

I have two versions of Twilight Princess non selects on the Wii, an A and a B

Nice catch. I did some more research and actually found five versions. It looks like there are three identifying features on the box and one on the disc. To the left of the product code on the box is another code (anyone know exactly what it's for?). First is the made in label. Right of the UPC is another 5 number barcode what changes between versions. The five digit barcode is mostly used for books to give suggested retail price, but that's certainly not what it's used for here. Finally, on the back of the disc near the center hole is a version code. More info here http://www.zeldaspeedruns.com/tp/knowledge/version-differences.
 

Made In	Box Code	UPC 5 Code	Disc Code	Ebay
Japan	62483A	00000	RVL-RZDE-0A-0 JPN	https://www.ebay.com/itm/143357225790
USA	61602A	00100	RVL-RZDE-0A-0 USA	https://www.ebay.com/itm/183896273881
USA	61602A	00100	RVL-RZDE-0A-2 USA	https://www.ebay.com/itm/143357242617
USA	61602B	00101	RVL-RZDE-0A-2 USA	https://www.ebay.com/itm/153601676892
USA	61602C	00102	RVL-RZDE-0A-2 USA	https://www.ebay.com/itm/133124326200

Disc codes are hard to read off of ebay listings. I only found about 7 I could read. So, if anyone wants to open their copy and see what box and disc code they have, please post below. I only found one 61602C version searching 200+ ebay listings (the rest are all pretty common). You may notice it was sold. I only had the Gamecube version of TP and I wanted Super Paper Mario anyway (other game in listing), so I bought it. I'll update the table with the disc code when it arrives.

Looking at my other Wii and Gamecube games it seems like the middle digit of the UPC 5 indicates where the game was made (0 = Japan, 1 = USA). The last digit indicates box revision (0 = A, ...). Also the number of the box code changes between country of manufacture. Now that I know what to look for I'll start to look for more variants for disc based games.

EDIT: For completeness here are the Gamecube and Wii Selects codes.
 

Made In	Box Code	UPC 5 Code	Disc Code	Ebay
USA	58684A	00100	DOL-GZ2E-0-00 USA	https://www.ebay.com/itm/20275244...
USA	74472A	00100	RVL-RZDE-0A-2 USA	https://www.ebay.com/itm/173963094087

EDIT2: My 61602C has arrived and it is version 1.2 as expected.

I found a new box variant for Link's Crossbow Training. I was only able to find the blue sided box version on ebay, but then I realized my copy has white sides. I've done a bunch more research on box variants and here's what I found.
 

Title	Made In	Box Code	UPC 5 Code	Disc Code
Wind Waker	Japan	50517A	00000	DOL-GZLE-0-00
Wind Waker	USA	50516A	00100	DOL-GZLE-0-00
Wind Waker [PC]	Japan	50517B	00001	DOL-GZLE-0-00
Wind Waker [PC]	USA	57818A	00100	DOL-GZLE-0-00
Wind Waker [PC]	USA	50516B	00101	DOL-GZLE-0-00
Collector's Edition	Japan	52938A	00000	DOL-PZLE-0-00
Collector's Edition	USA	52538A	00100	DOL-PZLE-0-00
OoT MQ	USA	50168A	00100	DOL-D43E-0-00
FSA	USA	54324A	00100	DOL-G4SE-0-00
FSA [PC]	USA	54324B	00101	DOL-G4SE-0-00
FSA [Big Box]	USA	54345A	00100	DOL-G4SE-0-00
SS	USA	75627A	00100	?
SS [CD]	USA	75798A	00100	RVL-SOUE-0A-0
SS [Remote]	USA	75631A	00100	RVL-SOUE-0A-0
PH	Japan	61332A	00000	N/A
ST	Japan	69175A	00000	N/A
OoT 3D	Japan	74524A	00000	N/A
OoT 3D	Japan	74524B	00001	N/A
OoT 3D [Selects]	Japan	103587A	00000	N/A
aLBW	Japan	81561A	00000	N/A
aLBW [GotY]	Japan	81561B	00001	N/A
aLBW [Selects]	Japan	107555A	00000	N/A
aLBW [Selects]	Japan	107555B	00001	N/A
MM 3D	Japan	83319A	00000	N/A
MM 3D [Selects]	Japan	110011A	00000	N/A
Tri Force Heroes	Japan	102479A	00000	N/A
HW Legends	Japan	103361A	00000	N/A
WW HD	USA	81115A	00100	?
WW HD [Blue]	Japan	101975A	00000	?
WW HD [Selects]	Japan	104186A	00000	?
Hyrule Warriors	USA	83662A	00100	?
Hyrule Warriors	USA	83662B	00101	?
TP HD	Japan	102472A	00000	?
BotW [Wii U]	Japan	103423A	00000	?
BotW [Wii U]	Japan	103423B	00001	?
BotW [Switch]	Japan	105211A	00000	N/A
BotW [Switch]	Japan	105211B	00001	N/A
HW: Definitive Ed.	Japan	107775A	00000	N/A

It was really hard to find information on disc codes. About one in 30 ebay listings have a legible code. I wasn't able to confirm any software revisions higher than 1.0 (besides the twilight princess stuff in my previous post). I know at least skyward sword has a 1.1 and a 1.2. See here https://www.reddit.com/r/zelda/comments/1zre2i/can_someone_t... .

Another way to tell the printings of the Oracle games (and Link to the Past on gba) is the type of box flaps they use. The later printings have a bottom in the similar style to NES boxes, a folding of various flaps, while the earlier printings use the style of flap that have grooves that catch the side flaps - similar to n64 boxes with built in trays. The kind that is super hard to open without creasing the flap. So, if you look at the bottom of the box and see a solid, flat surface it's the earlier release of OoS or OoA. Also, the top flaps are different too (earlier release using the same type of flap for the top flap as the bottom while the later release has the really nice solid flap).

Looked more into the NES zeldas, and I found some more variants.

TL;DR
Zelda 1: 10 box variants, 11 cart variants, 6 manual Variants, 14-16 total variants
Zelda 2: 5 box variants, 5 cart variants, 4 manual Variants, 6-8 total variants

Starting with Zelda 1 here's the box variants I found. Color denotes where the identifying mark is located. New SS = Screen shot on upper right, CR = copyright date, FS = For sale in...

Box	Rev-A	SOQ	NES TM	Zelda TM	GP	New SS	CR	Zip	FS	Box Code
1	No	Circle	TM	TM	No	No	87	98052	No	None
2	No	Circle	R	TM	No	No	87	98052	No	None
3	No	Circle	R	TM	No	Yes	87	98052	No	None
4	Yes	Circle	R	TM	No	Yes	87	98052	No	None
5	Yes	Circle	R	TM	Yes	Yes	87	98052	No	None
6	Yes	Circle	R	TM	Yes	Yes	87	98052	No	NES-ZL-USA
7	Yes	Oval TM	R	R	Yes	Yes	87	98052	No	NES-ZL-USA
8	Yes	Oval TM	R	R	Yes	Yes	87,89	98073-0957	Yes	NES-ZL-USA*
9	Yes	Oval R	R	R	Yes	Yes	87,89	98073-0957	Yes	NES-ZL-USA
10	Yes	Oval R	R	R	Yes	N/A	92	98073-0957	Yes	NES-ZL-USA-1

Next is cart list. MiJ = Made in Japan, CR = copyright date, RT = Red Text on back.

Cart	SOQ	NES TM	Zelda TM	Cart Code	MiJ	Screws	CR	Rev-A	RT
1	Circle	TM	TM	None	No	5	No	No	No
2	Circle	R	TM	None	No	5	No	No	No
3	Circle	R	TM	None	No	3	No	No	No
4	Circle	R	TM	None	Yes	3	No	No	No
5	Circle	R	TM	None	Yes	3	No	Yes	No
6	Circle	R	TM	None	Yes	3	No	Yes	Yes
7	Circle	R	TM	NES-ZL-USA	Yes	3	No	Yes	Yes
8	Circle	R	TM	NES-ZL-USA	Yes	3	85	Yes	Yes
9	Oval TM	R	R	NES-ZL-USA	Yes	3	85	Yes	Yes
10	Oval R	R	R	NES-ZL-USA	Yes	3	85	Yes	Yes
11	Oval R	R	R	NES-ZL-USA-1	Yes	3	85	Yes	No

And last the manual

Manual	Manual Code	Zelda TM	Zip
1	None	TM	98052
2	NES-ZL-USA-1	TM	98052
3	NES-ZL-USA-1	R	98052
4	NES-ZL-USA-1	R	98073-0957
5	NES-ZL-USA-1*	R	98073-0957
6	NES-ZL-USA-2	R	98073-0957

To determine probable CIB combinations I assumed that the things below should be the same across all items. It is hard to be sure, so I've also indicated my confidence. For the sake of the list of above, I included all likely combinations, and one of the probable pair.

Variants	On Ebay	C	I	B	SOQ	NES TM	Zelda TM	Rev-A	Zip	Code	Comments
Very Likely	X	1	1	1	Circle	TM	TM	No	98052	No	Only cart and box with NES TM
Likely		2	1	2	Circle	R	TM	No	98052	No	Only saw cart 2 sold as loose, but it probably went with box 2
Probably		2	1	3	Circle	R	TM	No	98052	No	Cart 2s are fairly rare, so I don't think it matches with the new SS box
Unlikely	X	3	1	2	Circle	R	TM	No	98052	No	Didn't see enough of this box to get a good idea
Very Unlikely		3	1	3	Circle	R	TM	No	98052	No	Didn't see any out of a decent number with box 3
	X	4	1	2	Circle	R	TM	No	98052	No	Didn't see enough of this box to get a good idea
	X	4	1	3	Circle	R	TM	No	98052	No	The last no rev-a cart and last no rev-a box
		5	1	4	Circle	R	TM	Yes	98052	No	First rev-a cart and box
		5	1	5	Circle	R	TM	Yes	98052	No	Cart 5 is rare. I've only seen a couple loose, never CIB
	X	6	1	4	Circle	R	TM	Yes	98052	No	Since cart 5 is rare, box 4 change probably changed later
	X	6	1	5	Circle	R	TM	Yes	98052	No	Last rev-a cart and box without code
	X	7	2	6	Circle	R	TM	Yes	98052	Yes	Only one circle seal, with code box. Also manual 2 because Zelda TM with code
	X	8	2	6	Circle	R	TM	Yes	98052	Yes	"
	X	9	3	7	Oval TM	R	R	Yes	98052	Yes	Only combination with old zip and oval TM seal/Zelda R
	X	9	4	8	Oval TM	R	R	Yes	98073-0957	Yes	I don't know what the * manual matches with
	X	9	5	8	Oval TM	R	R	Yes	98073-0957	Yes	"
	X?	10	4	9	Oval R	R	R	Yes	98073-0957	Yes	Saw cart/box 10 mostly with the * manual
	X	10	5	9	Oval R	R	R	Yes	98073-0957	Yes	"
	X	11	6	10	Oval R	R	R	Yes	98073-0957	Yes	Classic series (gray cart)

Now on to Zelda 2.

Box	SOQ	Link TM	CR	Zip	Box Code
1	Circle	TM	88	98052	NES-AL-USA
2	Oval TM	TM	88	98052	NES-AL-USA
3	Oval TM	TM	88,89	98073-0957	NES-AL-USA*
4	Oval R	TM	88,89	98073-0957	NES-AL-USA
5	Oval R	R	92	98073-0957	NES-AL-USA-1

Cart	SOQ	Link TM	Cart Code	CR
1	Circle	TM	NES-AL-USA	No
2	Circle	TM	NES-AL-USA	85
3	Oval TM	TM	NES-AL-USA	85
4	Oval R	TM	NES-AL-USA	85
5	Oval R	R	NES-AL-USA-1	85

Manual	Manual Code	Link TM	Zip
1	NES-AL-USA	TM	98052
2	NES-AL-USA	TM	98073-0957
3	NES-AL-USA*	TM	98073-0957
4	NES-AL-USA-1	R	98073-0957

Variants	On Ebay	C	I	B	SOQ	Link TM	Zip
Very Likely	X	1	1	1	Circle	TM	98052
Likely	X	2	1	1	Circle	TM	98052
Probably	X	3	1	2	Oval TM	TM	98052
Unlikely	X	3	2	3	Oval TM	TM	98073-0957
Very Unlikely	X	3	3	3	Oval TM	TM	98073-0957
		4	2	4	Oval R	TM	98073-0957
	X	4	3	4	Oval R	TM	98073-0957
	X	5	4	5	Oval R	R	98073-0957

EDIT: I found another cart (#5) with the help of rondy_.

With the GBA Four Swords, is the 100% or the 83% recycled the first print? I think in seeing the metallic on the left logo but want to ensure I'm correct.

100% should be the first print

I made another update to the list. Here is a run down of my changes.

NES: I found a new cart for Zelda 1 that is Rev-A but the text is all black. I've updated my details NES CIB research post. I'm still not happy with how the manuals are matched up, but it's the best I can do for now. 

SNES: I found another two Control Set Bundles. One has "Special Offer!" on the stick replaced with "Free!" (https://www.ebay.com/itm/302143414453). The other is just the -0 variant of the normal box (https://www.ebay.com/itm/183860995476). For good measure, here is the -1 "Special Offer!" (https://www.ebay.com/itm/264004207800).

Gameboy: I discovered that the -1 cart came with the -0 and -1 manual. I've found pictures of the -3 manual and Splain has seen the -2 manual. This would accound for another variant, but I haven't added it to the list since I don't know what cart it matches with. More documentation is here: http://nintendoage.com/forum/messageview.cfm?StartRow=181&am...

Gamecube: Did a lot more work going though console pack-ins. Since most of the pack-ins are just stickers on normal boxes I first researched those. Granted the pack-ins where not available for the entire lifetime of the console, so only a subset of these are possibly used in pack-ins. Here are all normal boxes I found. BR SS is the bottom right screen shot on the back of the box. Verified means I have found pictures with the box code. The rest I have only seen pictures of the color and BR SS. Finally, a code beginning with "C/GB" is made in China, and a code beginning with just "GB" is made in Japan.
 

Code	Color	BR SS	Verified
GB-DOL-S-KB-USA	Black	Kameo	Yes
GB-DOL-S-KB-USA-2	Black	Sonic Adv.	Yes
C/GB-DOL-S-KB-USA	Black	Sonic Adv.	Yes
C/GB-DOL-S-KB-USA-1	Black	Aggressive	Yes
C/GB-DOL-S-KB-USA-2	Black	Sonic Heros	Yes
C/GB-DOL-S-KB-USA-?	Black	Harry Potter	No
C/GB-DOL-S-KB-USA-5	Black	Goldeneye	Yes
GB-DOL-S-VTB-USA	Indigo	Kameo	Yes
GB-DOL-S-VTB-USA-2	Indigo	Sonic Adv.	Yes
C/GB-DOL-S-VTB-USA	Indigo	Sonic Adv.	Yes
GB-DOL-S-VTB-USA-?	Indigo	Aggressive	No
C/GB-DOL-S-VTB-USA-?	Indigo	Aggressive	No
?	Indigo	Sonic Heros	No
C/GB-DOL-S-VTB-USA-?	Indigo	Harry Potter	No
C/GB-DOL-S-PLB-USA	Platinum	Aggressive	No
C/GB-DOL-S-PLB-USA-1	Platinum	Sonic Heros	Yes
C/GB-DOL-S-PLB-USA-2	Platinum	Harry Potter	Yes
C/GB-DOL-S-PLB-USA-4	Platinum	Goldeneye	Yes

I'm sure I've missed some since Gamecube boxes are not usually pictured very well (especially the box code on the tab). The only Zelda pack-ins that I've seen backsides for are the black/indigo collector's edition (and carrying case). Of those I've only seen GB-DOL-S-VTB-USA-2 and C/GB-DOL-S-KB-USA-1 (Only the C/...-1 for Indigo). Again I'm sure there are more, but those are the only one's I've seen pictures of.

Switch: I was being stupid and thought that the Link's Awakening Limited Edition was available in the US too. So, I've removed that.