Here is a current list of repro makers and websites.  IF YOU KNOW OF ONE THAT ISN'T ON THIS LIST, PLEASE PM ME.  I don't check the posts in this thread so I will miss posting you if you post in the thread instead of messaging me directly.  Here is the list:

RetroZone makes NES and SNES repros and is the home of the famous Powerpaks.  Brian, aka BunnyBoy on NA, is the owner and they are headquartered in Redwood City, CA.  He does not answer PM's so please do not PM him, he is extremely busy:
http://www.retrousb.com

The NES Dump does NES repros and a few SNES repros.  Joe is the owner, coinheaven on NA, and currently has the LARGEST list of NES repros out there.  His has quality work and he has a fast turnaround:http://www.thenesdump.com/

NES-City makes repro boxes, labels, and manuals.  His user ID on Nintendo Age is fsped09.  I love his Final Fantasy repro boxes as well as his 8-bit XMAS repro boxes.  He can also do powerpak boxes and special requests.  He is a member here on NA.  He now does 8-bit XMAS boxes and boxes for most of the retrozone items as well as manuals and custom labels.  He does incredible work and his NES boxes are the only ones custom made out there that have exact specifications to a regular NES released box.  He hand cuts all his boxes, labels and manuals.  Here is his website:
http://www.nes-city.com
Here's his thread on NA:
http://www.nintendoage.com/forum/...

Rose Colored Gaming makes phenomenal repros.  They do their own custom art as well as posters, maps and amazing full CIB releases.  They also do custom consoles and homebrews not sold anywhere else.  Check them out:
http://www.rosecoloredgaming.com/...

Flashback Entertainment is an amazing company making NES & SNES repro games.  They have unique hacks (exlusive to them) and their quality is phenomenal!  I've bought from them many times and I love their work.  They have one of the best zelda hacks I've ever seen and it's exclusive to them.  Check them out:
http://www.shopflashbackgames.com...

Clarky_N64 makes repros for NES.  He also does a few maps/posters as well.  His repros are very inexpensive if you provide a donor.  He offers full painted carts with new labels also if you just want to buy repros.  He has a for sale thread here on NA:
http://nintendoage.com/forum/mess...

NES Reproductions makes a variety of NES repros and homebrews.  This is Leon's website and he does have some custom labels that are unique:
http://www.nesreproductions.com/

OCDGamer makes repro carts.  He is a member here on NA.  He does his own custom labels and the carts come out beautifully.  I currently buy every different one he makes, they are that good.  He now has a website as well as a NA thread for his sales.  He does excellent work and his prices are extremely good.  He currently has a HUGE selection of NES games which some I have only seen him sell.  He is going to be working on SNES repros also so if you need something made, he may be the person to ask:
http://www.nintendoage.com/forum/...
http://www.ocdreproductions.com/...

The Nolan Bros here on NA, aka MrMark0673 & BeaglePuss here on NA, provide top notch Sega repros for sale on Sega Age.  MrMark is Mark Nolan and BeaglePuss is Matt Nolan and YES they are twins.  They are the premier Sega repro makers and do top notch work.  They are also very large prototype collectors and will often do a release from a prototype so contact them if you have an unreleased game, they will help you release it or buy it from you:
http://segaage.com/forum/messageview.cfm?catid=43&thread...

Millerjm2 here on NA makes some AMAZING CIB repros.  He also does custom work of future released titles.  He sells some of his CIB's here on NA:
http://www.nintendoage.com/forum/messageview.cfm?catid=6&...
He is now making full CIB sets minus the game:
thisroomisanillusion.com

Second Dimension: owned and run by Dra600n here on NA.  He makes his own homebrews for Sega and on a rare occassion dables in NES or other.  He's an amazing guy and has some quality stuff.  He also sells Sega PCB boards. 
http://www.second-dimension.com...

Retro-1up-junkie makes PAL repros for SNES.  They also offer a translation list for the games they have translated.  Check them out:
http://www.retro-1up-junkie.co.uk... Retro Fools is a shop I found on etsy that does some really cool NES repros and they are the only repro maker I've found that makes the wireless NES router.  He goes by Megabyte52 here on NA.  They also do their own labels:
https://www.etsy.com/shop/RetroFo...
http://www.nintendoage.com/forum/...

Retrostage is another repro maker of repro boards.  They don't sell full blown repros anymore but will provide the boards.  They have a website and a thread on NA:
http://www.nintendoage.com/forum/...
www.retrostage.net

Lost Classics - I found this group at the PRGE 2011 expo and they currently make repros for Game Trader.  They have a lot of custom made labels that are unique.  They now have a website and you can order neet games such as Star Fox 2 and other sought after repro titles.  At the 2012 PRGE they had a variety of SNES repros that most repro makers don't make.  Their work is superb:
http://www.lostclassicvgs.com/...

Webmeister is on atariage.com and his info was shared with me recently.  He makes a LOT of SNES repros including the hard to get Star Ocean and Starfox 2.  I have yet to buy from him so I'm not sure on the quality but it looks like he includes the games and media cases with slip art for very reasonable prices.  Definitely check him out:
http://www.atariage.com/forums/to...

Pootle on Digital Press forums does some custom NES and SNES Repros.  He sells some unique items that noone else makes so it's worth checking out:
http://www.digitpress.com/forum/showthread.php?t=120604&...

Beep Beep Technical Repoduction Games - Goes by Hubz here on NA.  He has a LOT of NES titles that he makes repros of.  Check out his thread:
http://www.nintendoage.com/forum/...

Depot Retro is a newer repro making site that has a LOT of SNES titles and some that I haven't seen before like Ys V.  He's got a lot of the up to date newer SNES stuff and it looks like he's going to be doing some NES stuff soon.  He goes by darknezz19 here on NA.  Here's his site:
http://www.depotretro.com/...

64 Drive is the flash cart for the N64.  This is "like" the powerpak for NES and SNES except this is for N64.  Not all roms work with it and there is a long wait from when you order until you receive it.  I just received mine 2/13/2012 and I ordered mine on 9/7/2011 just to give you an idea of how long it may take to receive yours.  Here is the website to order and get more info:
http://www.retroactive.be/64drive... Heavyw8bit makes NES music development carts.  They currently have "Beatbox" and "NESK-1" which allow for some musicians to make homebrew music:
http://www.heavyw8bit.com

Ninstrument makes custom NES Synth carts to do custom Midi making music.  They even have a cool controller combo thing that costs $295 but can do a lot.  Go check them out:
http://www.ninstrument.com/...

Kitsch-bent is a website that sells a gameboy type powerpak that connects through USB and a gameboy advance one.  There are plans for a N64 flash everdrive player as well:
http://store.kitsch-bent.com/ Stone Age Gamer makes Everdrive carts for Sega, SNES, Nintendo 64, Sega Master System and Game Gear.  They come CIB and looks pretty awesome!  They also have a digital magazine they publish as well as selling games:
http://stoneagegamer.com/

Uncle Tusk - In my opinion one of the the best repro box makers out there.  Top of the line printing and the boxes have the folds in them.  It feels just like a factory made NES original box when he makes one.  Very reasonable prices also:
http://www.uncletusk.com/

Callanbrown - is a repro maker I recently found out about.  He hosts a website that does in depth descriptions on how to make certain repros.  It's really a "how to" guide for those interested in making their own repros.  He does sell some repros actively:
http://callanbrown.com/

8 Bit Evolution - Goes by mattyjmania here on NA.  They make custom boxes and CIB's for SNES, NES and Genesis repros.  They also do modded consoles and some other cool stuff.  Unique artwork and designs.
You can visit their website at:
http://8bitevolution.com/
He also has a NA sale thread showing some of his goods here:
http://www.nintendoage.com/forum/...

NES4life here on NA makes repro games.  Here's his thread:
http://www.nintendoage.com/forum/...

Save Point Videa Games known as SavePointVG here on NA does mostly SNES repros.  He offers a $30 SNES repro service or 3 for $75.  Here is his NA FS thread and his website:
http://nintendoage.com/forum/mess...
www.savepointvideogames.com...

8-bitBishop here on NA is selling a bunch of amazing NES repros.  I'm placing a nice size order since there are a lot of items unique to just him.  I recommend you all keep your eyes on this repro maker for some cool new stuff to come out soon.  His prices are very fair:
http://www.nintendoage.com/forum/...
He has a new website that should have gaming and updates coming soon:
http://bishop-bros.com...

K1ng_aw - a seller I found on ebay UK who makes custom maps, posters, memory cards, etc.  Here is a link to his for sale items on ebay:
http://www.ebay.co.uk/sch/k1ng_aw/m.html?hash=item2a197ad68a...

1upgames_co_uk - another seller on ebay UK who makes custom repro boxes and manuals.  He can also do different languages as well as NTSC or PAL versions:
http://www.ebay.co.uk/sch/1upgames_co_uk/m.html?hash=item43a...

WickedClownNz - member of youtube who makes custom repro games.  Here is a sample video:

Chip Master - makes SNES and NES repros.  They have a very large variety and their prices are extremely fair.  I was made aware of this company by another member on NA and they stated that the labels are always clean and nice and the carts don't have dirt or anything else on them.  This seems to be an excellent repro maker.
http://chipmasters.us/...

Game Reproductions is run by necrosaro420 here on NA.  He has a bunch of NES repros and the largest SNES repro collection for purchase.  It does take about 30-60 days (one user reported over a year's wait) on average before you receive your items so please keep this in mind, and buy at your own risk.
http://www.gamereproductions.com/

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CLOSED

Time Walk Games has custom CIB repros.  The company is owned by Spencer, aka nesrepro on NA, and they are located near Cleveland, OH.  They currently have NES repros and are making SNES repros.  They are taking new orders again and they now get their boxes FACTORY MADE!!!  That means that these will be the closest thing to original that there can be since they are being made the same way.  Check out some of his new games:
According to their website as of 01.27.2014, they website states that they are no longer taking new orders.
http://www.timewalkgames.com/ Site down on 3/5/14

Windy Gaming is another company that makes repros for SNES & Genesis.  I haven't bought from them yet but they have some unique titles I haven't seen anywhere else.  They also offer a Star Fox 2 overclocked SNES cart.
You can find them at their website:
http://www.windygaming.com/collec...
They are no longer doing repros

leatherrebel5150 here on NA does some awesome looking repros.  His repros are pretty competitive, he does color carts and tons of unique labels.  He also has a lot of titles that I haven't seen anyone else carry including 5+ different Castlevania games.  Check him out: As of 5/12/14 ceasing reproduction making. 
http://nintendoage.com/forum/messageview.cfm?catid=6&thr...

Chilant - member on NA that offers a $25 SNES repro service:
http://nintendoage.com/forum/messageview.cfm?catid=6&thr...

RetroQuest - UPDATE - THEY WILL BE CLOSING VERY SOON SO BUY FROM THEM WHILE YOU CAN!!!
A new repro website that will do SNES Repros.  Pretty neat and exclusive stuff.  There are some unique homebrews by Piko sold here.  Piko is no longer a part of RetroQuest btw so please do not bother him regarding their repros.  I checked out the website as well as his facebook page and he has put a lot of work into them:
http://retroquestgames.com

Repro Paradise - SnesTalgia here on NA runs a website called Repro Paradise specializing in mostly SNES but they are bringing some NES to their shop.  They have some unique SNES repros so go check them out!
www.ReproParadise.Com...

ReproCarts is a PAL based company that does some really cool repro SNES carts.  They have all the big hits as well as several less known titles.  The owner goes by NerdPrincess here on NA:
http://www.reprocarts.com/...

Piko (BANNED) - He is a member here on NA who makes SNES repros and is even doing some crazy unique stuff that will be out soon.  Here is a FS thread he has on NA of completed repros:
http://www.nintendoage.com/forum/...

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Thanks. I'll be bookmarking this.

Thanks a lot man.

I just ordered Super Tecmobowl 2012 from Time Walk Games I can't wait to get it.

nice list, im still looking for someone who can make personal copies of SNES. I really want a Rendering Ranger 2 for my NTSC SNES, instead of getting a famicom and shelling out mass money for the game

I've been waiting for a website to have a Parallel Worlds repro for a decent price.

Bookmarked. Thanks a ton, man!

EDIT,

nm.  It was posted.

Bookmarked it as well Thanks

I'd like to think of Matt and myself as the premier Genesis Repro guys at the moment, though others may disagree. Not a company and no dedicated website, but you can see what we offer here:

http://segaage.com/forum/messagev...

We've made well over 1,000 repros over the years across NES and Genesis, as well as the production of one legitimate Home Brew release in Hangman SG, so I think that gives us some street cred. If this doesn't belong here because we don't have our own website, we can certainly remove it.

Yep, The Brothers Nolan deserve to be on this list for sure. Nothing but A+ quality work and service there. I think a dedicated thread should qualify.

Of COURSE you are added to the list.  I put you down as the Nolan Brothers since that is what everyone refers to you two as anyways.  I do have some of your repros and they are awesome work.

I do want anyone who makes repros actively (that wants to be published with it) whether or not they have a website.  My goal is to keep a running list so everyone knows who makes this stuff.  When I started with NA I had a heck of a time finding these companies and I find out about new ones all the time.  I felt it was time to have a comprehensive list of companies with a brief explanation.

I think it should be safe to say while there's no website for the services, DRAKON a member here (and elsewhere) is in the process of offering up a special kind of overclocked legit games and shortly with Star Fox 2 offering up an overclocked and reproduction service of that game. I know you can send him a DOOM game and he can for like $30 overclock the FX2 chip and get that thing running really smooth compared to the stock cart.

I think it deserves a listing with a link to just a link to his profile so someone can PM him for those services.

Bumping this up for more people to see

B.A., a mod on NA, is selling a unique Stadium Events repro for anyone interested. This should be the ONLY Stadium Events repro sold IMO:

http://www.nintendoage.com/forum/...

I've already contacted him and made arrangements to buy it.

Every crappy collection needs a crappy SE repro

What about Coinheaven? I've always liked his stuff.

coinheaven aka Joe operates thenesdump.com

Now you have your Stadium Events.  I thought you said you weren't considering it a variant ;-)

If you read the info next to thenesdump it shows coinheaven as the owner.

I try to put everyone's NA user id if they are on here so everyone can contact them here with the exception of bunnyboy of course.

x2

x3 they are at the forefront of amazing awesomeness! /highfive guys

Should I add makers of flash carts to the list? There are a variety of companies that have flash carts for all the systems up through Nintendo DS. I figure people may be interested in those also.

I just updated the list with "Stone Age Gamer".

Please PM me if you have any other repro makers or flash drive makers.

Timewalk has closed up shop.

http://www.timewalkgames.com/...

"Hi All. I am no longer taking orders for games. All previous orders that have been placed have been finished. You should be receiving it shortly. Feel free to e-mail me via the contact page for updates on any outstanding orders.

Unfortunately my life has become to busy to continue doing this. It is a hobby for me. I love retro-gaming and would love to keep the older systems alive, however at this point, I'm having a really hard time keeping up with orders and shipping and customers support etc. and as much as I'd like to quit my day job to keep doing this, the wife says no Thanks and I will still be posting to Nintendo Age to keep up with you guys! -S"