I recently returned from a week-long stay in Tokyo. Naturally one of the things I did was to check out some of the retro game stores Tokyo has to offer, so I thought I'd post some up-to-date (as of early August 2014) comments about the stores I visited in case anyone else here is going to Tokyo soon, or just has a general interest in the situation.
Note that I was interested mainly in games for the Famicom, Super Famicom and Gameboy - and mostly in japanese versions of games that were also released here in Europe (think big titles by Capcom, Konami, Sunsoft, etc). I hardly looked at games for other systems, like the Mega-CD, PC-Engine or Dreamcast. Keep in mind that the selection of games can vary from day to day, as items are sold and new ones come in.
For anyone reading this in the future: the exchange rates at the time of writing are about 102 yen per USD and about 137 yen per Euro.
Mandarake Galaxy (Nakano Broadway)
This was the first store that I visited. They had a pretty decent selection of FC games, both boxed and loose ones. They also had a bunch of boxed SFC games, but nothing I was interested in at the prices they were asking. They did have a boxed copy of GB Dracula Densetsu for 2500 yen, which I unfortunately didn't buy. At the back of the store they had a few shelves with unsorted FC and SFC carts at, IMO, fair prices (e.g. SMB3 for 500 yen).
Tomato Land (Nakano Broadway)
Located at the 3rd floor of the same shopping center where you'll find the Mandarake Galaxy store. They don't have as many games, and in particular not that many boxed ones. There was a bargain bin with FC carts starting at 100 yen, but it was mostly full of crap games. I did pick up a SwanCrystal here with box and manual.
Mandarake (Akihabara)
The games were located on the 6th floor. The selection of games was pretty good - almost as good as Super Potato's. The prices in general were slightly lower. The aisles are pretty narrow, so you'll often find yourself having to move over to make way for other people. This was the store were I spent the most money (e.g. a copy of Hebereke with box for 3800 yen).
Super Potato (Akihabara)
Still had the best selection, although it was rivaled by Mandarake. I guess you're not that likely to make any bargains here, but I did find a copy of Gargoyle's Quest II for about 2400 yen, which I think was reasonable since one of flaps on the box was a bit damaged. At the top floor they had a small arcade where I spent some time playing Dynamite Deka.
レトロげーむ (Akihabara)
Located next to Trader 3, not far from the Game Taito Station arcade. Not sure why they wrote "げーむ" that way. In any case, they had quite a few boxed FC games, and a few for SFC/GB as well. Narrow aisles.
Liberty (リバティー) (Akihabara)
Located one block from レトロげーむ. The games are on the 2nd floor. They had very few boxed FC/SFC games. There was a shelf with FC carts for 300 yen each, but I didn't bother browsing through all of them.
Trader (Akihabara)
I didn't buy anything here. They had quite a few loose FC/SFC games, but IIRC the carts were standing sideways in plastic boxes without labels, so you had to pull each one out to see what game it was, which was very time-consuming.
Friends (Akihabara)
Seemed a bit unorganized.. games everywhere, some of which didn't appear to be sorted. But a pretty good selection of FC games. I picked up a copy of Rockman 6 with box and manual for 5000 yen. I also saw a boxed copy of Batman for 3500 yen, but didn't have any cash on me at the time and it was near closing time. For some reason they did not add the 8% sales tax at the register. I guess either they had already included the tax in the listed prices, or they weren't following tax regulations
I also went to Sofmap's main store in Akihabara, but as far as I could tell they didn't have any games for consoles older than the DS/PSP.
If you're going to the Akihabara stores I recommend taking the Ginza line to Suehirocho, instead of going to Akihabara Station. As you exit the subway you'll have Friends right across the street (or around the corner, depending on which exit you use). After that you can just walk down the Chuo Dori and its side streets to get to all the other stores.
Keep in mind that many stores do not accept credit/debit cards issued outside of Japan. What's worse, some ATMs also don't accept foreign cards, so you'll have to find one that does. There were a few suitable ATMs near Akihabara station.
Note that I was interested mainly in games for the Famicom, Super Famicom and Gameboy - and mostly in japanese versions of games that were also released here in Europe (think big titles by Capcom, Konami, Sunsoft, etc). I hardly looked at games for other systems, like the Mega-CD, PC-Engine or Dreamcast. Keep in mind that the selection of games can vary from day to day, as items are sold and new ones come in.
For anyone reading this in the future: the exchange rates at the time of writing are about 102 yen per USD and about 137 yen per Euro.
Mandarake Galaxy (Nakano Broadway)
This was the first store that I visited. They had a pretty decent selection of FC games, both boxed and loose ones. They also had a bunch of boxed SFC games, but nothing I was interested in at the prices they were asking. They did have a boxed copy of GB Dracula Densetsu for 2500 yen, which I unfortunately didn't buy. At the back of the store they had a few shelves with unsorted FC and SFC carts at, IMO, fair prices (e.g. SMB3 for 500 yen).
Tomato Land (Nakano Broadway)
Located at the 3rd floor of the same shopping center where you'll find the Mandarake Galaxy store. They don't have as many games, and in particular not that many boxed ones. There was a bargain bin with FC carts starting at 100 yen, but it was mostly full of crap games. I did pick up a SwanCrystal here with box and manual.
Mandarake (Akihabara)
The games were located on the 6th floor. The selection of games was pretty good - almost as good as Super Potato's. The prices in general were slightly lower. The aisles are pretty narrow, so you'll often find yourself having to move over to make way for other people. This was the store were I spent the most money (e.g. a copy of Hebereke with box for 3800 yen).
Super Potato (Akihabara)
Still had the best selection, although it was rivaled by Mandarake. I guess you're not that likely to make any bargains here, but I did find a copy of Gargoyle's Quest II for about 2400 yen, which I think was reasonable since one of flaps on the box was a bit damaged. At the top floor they had a small arcade where I spent some time playing Dynamite Deka.
レトロげーむ (Akihabara)
Located next to Trader 3, not far from the Game Taito Station arcade. Not sure why they wrote "げーむ" that way. In any case, they had quite a few boxed FC games, and a few for SFC/GB as well. Narrow aisles.
Liberty (リバティー) (Akihabara)
Located one block from レトロげーむ. The games are on the 2nd floor. They had very few boxed FC/SFC games. There was a shelf with FC carts for 300 yen each, but I didn't bother browsing through all of them.
Trader (Akihabara)
I didn't buy anything here. They had quite a few loose FC/SFC games, but IIRC the carts were standing sideways in plastic boxes without labels, so you had to pull each one out to see what game it was, which was very time-consuming.
Friends (Akihabara)
Seemed a bit unorganized.. games everywhere, some of which didn't appear to be sorted. But a pretty good selection of FC games. I picked up a copy of Rockman 6 with box and manual for 5000 yen. I also saw a boxed copy of Batman for 3500 yen, but didn't have any cash on me at the time and it was near closing time. For some reason they did not add the 8% sales tax at the register. I guess either they had already included the tax in the listed prices, or they weren't following tax regulations
I also went to Sofmap's main store in Akihabara, but as far as I could tell they didn't have any games for consoles older than the DS/PSP.
If you're going to the Akihabara stores I recommend taking the Ginza line to Suehirocho, instead of going to Akihabara Station. As you exit the subway you'll have Friends right across the street (or around the corner, depending on which exit you use). After that you can just walk down the Chuo Dori and its side streets to get to all the other stores.
Keep in mind that many stores do not accept credit/debit cards issued outside of Japan. What's worse, some ATMs also don't accept foreign cards, so you'll have to find one that does. There were a few suitable ATMs near Akihabara station.