I have dealt with a few vendors away from the main stores:
Baen - Great customer-friendly setup, with freebies, good prices, redownloads and gift codes. Their range is quite narrow, and if anything they give too much away. I kind of had to force myself to buy something from them a few months ago because they deserved it. I still have a mountain of freebies to work through.
Book View Cafe - Again good prices, typically. Good variety but quite limited range. I've bought three books from them, and there isn't much else there that I want. They used to offer redownloads, but the new store does not, and it also only offers one of the two main formats now. I'm still happy to buy from them.
Poisoned Pen - I've only bought from them on their 99c offer, and I haven't actually read anything yet. Similar store setup to BVC: no persistent account with redownloads.
Wildside - I've yet to buy anything direct from them, but I will next time I want one of their books. Good prices on some backlist SF (I think it was $3 for the short Brian Stableford novels I bought). They also seem to repackage PD work. I had a good response from them when I emailed about a missing book on Amazon UK. Their website isn't much good for browsing, and they also split Kindle and EPUB.