Mostly guitar/instrument related, but here's a few things if you're visiting Tokyo:
Jinbōchō - a district/suburb, has an amazing street of instrument shops, including some incredible vintage guitars (with incredible prices to match).
Musicland Key (
http://wikimapia.org/13095912/Music-Land-KEY-Shibuya) - all new stuff, 5 floors of browsing including a hi-tech/recording floor.
Walkin Guitars (
http://www.walkin.co.jp/) - beautiful guitars, including really well presented second handers, generally good prices. Really nice guy who runs it, but impossible to find it!