Yeah, a cheezy title - I know. This is an absolute must-see for book lovers though: Book Town Jimbou.
The site's Jimbou Navi section features a nice and easy-to-use flash map that comes in handy if you're searching for bookstores specialized in specific literary genres. There's also an "old books" database, where you can search on title, author, etc. Great for those who want to do some research before diving into the Jimbou jungle - surprisingly, online shopping functionality is also available, so you can do all your Jimbou shopping from home.
And then my favorite part: a tour around 151 (!) book stores, giving you an idea what you can buy for a 3000 Yen budget. The presentation format is great, and the section's individual items are linked with the earlier mentioned Jimbou map and database. Good stuff. (Minor nitpick: those terrible