There are two true card shops in Akihabara, a Mint/Yellow Submarine store found in the Radio Hall building near the JR station, and Wrappers, found a few minutes away from the rest of the Akihabara action.
Wrappers recently rearranged their store, which I realized when I went looking for some more oddball-ish cards for a trade in November.
So how did the store change? I'm not sure if they got rid of anything or just reorganized the space, but the trading card section is now much smaller, and there is a larger space devoted to CCG cards. I realize that I haven't made a post about this store anyway, but readers of NPB Card Guy's Japanese Baseball Cards probably saw his post (with photos) about the store. I would guess they cut back on some of the complete sets or just reorganized that area, as the boxes and boxes of singles still remain. I'm a little worried they might try to clearance some of it out, though, so I'll probably make a trip again soon to compare. They are still stocking new cards though, so they aren't disappearing anytime soon as a baseball card store.
Here is their current (as of late November) business card:
their blog in Japanese if you'd like. Store hours are 12-8 weekdays, 11-7 on Saturday, closed on Sunday. Expect to pay 50 yen per card for common singles, though non-BBM/Calbee cards and older inserts seem to be all over the place as far as price to value. Your mileage may vary.