The best address for used books, especially manga in Japan, Book Off's prices are among the lowest anywhere. Starting at 100 Yen, carries all kinds of titles, mostly older books, but newer titles can be found as well, mostly good to excellent quality. They also sell CD's, video games and DVD's.
Book Off is a good source to complete your collections, or stock up on other series you are interested in for a low price. Just don't expect very much money when you try to sell your used titles again.
The store has been heavily criticised by some publishers for undercutting their profits by selling used books (reasoning every used book sold means one less new book sold), but praised by literates and book critics alike for keeping out of print titles available. In Japan, most publishers don't keep stock of the books they publish so that once initial orders are filled, and sold out in stores, the book is unavailable until reprinted, which may take a while, if ever.
There are Book Off stores all over Japan, and there is even one in the US, in NYC on 41st Street, near 5th Ave (Thanks to asterphage for the last bit of info).