Super Potato - probably the most retro chain of game stores in Japan. The Akihabara Super Potato has 3 floors which are dedicated to games throughout time - everything from the Famicom to PS3. You can even pick up some Nintendo Game Watch.
Was over there last week filming for Culture Japan which brought back a load of memories. If it wasn't for the Sega Megadrive, I may not have encountered Japanese culture at the right time as you read in the How did you become interested in Japan? post.
Was also nice to bump into a load of comrades in the store too.