I pretty much ignored ebooks.com until Agency pricing took off. Their books are all publisher suggested price and I've only gotten the 20% off to work on a single book. When Agency books are on sale, though, they're typically on sale at ebooks.com, too. Their DRM is strictly ADE, their website makes sense, and they're happy having me download books to my PC without needing a special device, all of which seem too much to ask the others. Christianbook is a close second, but they only have Christian books.
I typically use
eReaderIQ for the books that I want. I used to feel guilty because their revenue came from affiliate links, but Amazon killed eReaderIQ's affiliate account, so now it doesn't matter.