http://powells.com/

It's my personal preference, but I like Powells for book stuff. It's a local company, not an international chain, which is active in their local (Portland, OR) community as well as overseas, like donating old textbooks to 3rd-world countries. The site has Very Good employee recommendations, author interviews, and the like, and has things like 16th century bibles, limited edition Stephen King novels, and other fabulous stuff. Heck, their rare book room has a volume worth more than my house!

Plus, bibliophiles, if you're in the Portland area it's a new-and-used-book store over 70,000 square feet!! No I don't work there, but I've been going since before I was a teenager and I love them.