Great info, Maciamo, thanks a lot!

I bought most of my books at Kinokuniya in Shinjuku. They have a huge assortment of J-related titles (not only). I remember one huge bookshop in Ginza (looked kind of old-fashioned, multi-storied), I hope that's the one that has been closed.

If you are looking for antiquarian books, there's a small store off Aoyama-dori, direction Shinjuku (forgot the street's name, but there's a little Italian coffee shop right opposite). I've found dozens of cheap books there, some first editions by Seidensticker, great stuff. I also heard that Kanda is supposed to the no.1 place for antiquarian books.