This site allows you to search their database of 1,200,000 Japanese titles and 1,800,000 foreign titles and place an order. Fee based service. Maruzen Includes Japanese and foreign books. You need a Japanese operating system and a password to search. For the present, orders are accepted only from people in Japan.
Individual rates are reasonable.
Paragon Book Gallery Specializes in Asian arts and Asian studies. Sasuga Japanese Bookstore Sasuga receives its publications directly from the Japanese wholesaler, Tohan Inc., in Tokyo and has access to virtually anything published in Japan. Their website includes a searchable database of their catalog. They also provide magazine subscriptions. Tokyo Kosho Kumiai A guide to Tokyo's used bookstores.