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Junkudo
2-15-5 Minami Ikebukuro, Toshima-ku, Tokyo 171-0022
http://www.junkudo.co.jp
email: info@junkudo.co.jp

8th floor has all the educational materials including products by Kumon (so includes dictionaries and some other things in English and other languages)
9th floor has all the foreign language books and magazines
This is a huge store!
I've been lucky a couple of times now while trying to find kanji study cards, etc. for my daughter in that many of the staff on the 8th and 9th floors are bookworms, study English, and can even speak some!

This is closer to where I live than going down to Shinjuku (Kinokuniya books) or Shibuya (Tower Records).
There is also a Tower Records at Ikebukuro, but I get the impression that the book section is smaller than the one in Shibuya.

Another choice is in Takadanobaba --
Biblos F.I. Bldg. 5F, 1-26-5, Takadanobaba, Shinjuku-ku, Tokyo 03-3200-4531
or did someone say that Biblos is closed?

There is also a Biblos within the Seibu department store at Ikebukuro (on the 4th? floor), but I don't have a phone number for this one.

Books Sanseido has foreign books in some stores http://www.books-sanseido.co.jp. They have two locations with cafe inside the bookstore.

For a very comprehensive and often updated list of bookstores inside the Yamanote line (Tokyo) look at this list provided by Evelyn Leeper (who has a compilation copywrite on it). There is a small critical description included of each bookstore on the list.
http://www.geocities.com/Athens/4824/jp-tokyo.htm