From Shinsaibashi station in Osaka, take exit #7, which takes you out to the front of a big department store. Take a right (south) down the large, tree lined, Midosuji Boulevard. Walk past Berlitz and Citibank and look for the big Vivre 21 Department store sign acros the street. At the first street after Vivre, take a right. Walk down a few blocks. Time Bomb is on the right, across from the Asahi Hotel, before you go under the highway. Cool stuff is in the Basement (entrance below the outside stairs) and used stuff on the third floor. To get to the 3F, go in the door on the sidewalk side and take the elevator up.
King Kong, Namba
Just around the corner from Time Bomb, King Kong Records has lots of everything: J-Pop, Japanese and Western indie, punk, hardcore, techno, underground and experimental music. Time Bomb may have it over King Kong in unusual and great experimental music, but Time Bomb has nothing on King Kong's decor and store music. Although not a particularly big store, King Kong has about three or four seperate sound systems going at once, creating a truly disorienting musical experience. I also have NO idea how they sort their stock. It seems to be vaguely arranegd by time period/style, but after that is anyone's guess. It doesn't seem to be alphabetical in either Japanese or English.
From Time Bomb, head back towards Midosuji, then take the first right, heading towards Tower Records. King Kong is on your left.
Beaver Records, Kyoto
Not only does this place have the best used CD collection I found, it also has a great name.
Take the Keihan line to Shijo station in Kyoto, take one of the bridge exits, head across the river. Go across Kawaramachi, the large street that runs parallel to the river, and keep heading straight. Take a right into the first covered shopping street. Take another right at the Mr. Donut. Beaver is under an outhang on the left. Used experimental stuff is in the back next to jazz.