Yeah, buying second hand in Japan is almost like buying new stuff. While my (Japanese) wife and I lived in Japan during 2010, I bought a lot of stuff off Yahoo auction. Japanese people seldom use Ebay, but Yahoo auction is quite popular.
I bought two DAP's from Yahoo auction, a Kenwood HD20GA7 and a JVC/Victor XA-HD500, along with 4 ear-/headphones (ATH M50, ATH ES7, ATH CM700TI & Pioneer SE-EX9). The ATH M50 reeked of smoke and the ATH CM700TI earbuds were a bit dirty, but after changing earpads on the M50 and cleaning the CM700TI, they were like new. Everything was also a lot cheaper than buying new...
As have been mentioned here, there are places such as Book Off, which sells used books, manga, CD's, DVD's, toys, video games etc, and Disk Union which is a chain of second hand CD and DVD stores. If you go to Topkyo and Akihabara, there's Super potato which is like heaven if you like retro video games.
I found this on Youtube:
I found this on Youtube as well, from the Yodobashi store in Osaka. I went to Osaka last year, but it was just a day trip and we didn't have time to go into the Yodobashi store. Dang! I want to go to Osaka again!!!
Edited by Danneq - 8/15/11 at 4:52am