Tokyo
From BOOK STORE WIKI
Jimbo-cho<-the biggest bookstore area in Asia.
Japanese Bookshop Chains
Junkudo
http://www.junkudo.co.jp/mj/store/store_search.php
Kumazawa
Keibundo bookstores
http://www.keibundo.co.jp/shop/index.html
LIBRO
Toranoana
Book Off
The biggest second hand bookshop chain
GEO
Second hand book&CD chain