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If you're into science fiction/fantasy/horror, my favorite is easily Weightless Books and Wizard's Tower Books.
They're a publisher, so not sure if this counts, but the Angry Robot Bookstore is also great (although obviously, they only stock their own eBooks).
I also occasionally shop at Baen eBooks.
Edit: What I mentioned above are free from geo-restrictions, which is my problem with sites like B&N (doesn't sell to me at all) or iTunes (mostly public domain books at the local iBookstore).
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