Amazon.co.jp: Amazon in Japan. Article descriptions are in Japanese, but account setup, shopping, and checkout available in English.
GJ*Photobooks: Sells Japanese out-of-print photography books published in the 1960's and 1970's. Based in Urawa City, Saitama.
Good Day Books: New and used books, located in Ebisu, Tokyo.
Infinity Book Store: Used books in the English language available throughout Japan.
Kitazawa Bookstore: Tokyo bookstore offering new and antiquarian books. Online catalog.
Mitsukatta: Shopping site holding the entire amazon.co.jp catalog. Navigate in English, Japanese, Korean and Chinese.
Peek - A - Book Nook: English used bookstore in Hiroshima City. Offers book buying, selling and trading; searcheable database and online ordering.
The Japan Page.com: Kodansha International's online book website.
Tokyo Stories: Provides entertaining glimpses into the lives of foreigners in Tokyo. With excerpt and online ordering instructions.