Powells - Combine a huge selection in new books, many at sale prices, with a nearly just as large inventory of high quality used books, tons of rare titles, a free shipping offer, and a tax charge that lets me get my books here in Canada without paying duties, and you've got the best damn book store on the 'net. If you're planning on buying a bunch of stuff, this is the place to go.
Book Closeouts - A somewhat smaller inventory, but amazingly low prices on unused books, including some harder-to-find ones. Shipping is charged but low, and their second, Canadian warehouse means that again I don't have to pay duties.
Advanced Book Exchange - The place to find used books. If it's out there, you should be able to find it here. Most listings are thorough and you can search the inventories of individual booksellers as well as the entire site.
Happy shopping! ;)