Amazon books are in azw or topaz format (which I think is a variant of the first - someone will correct me if I'm wrong). Overdrive books are *usually* epub or ADE pdf format, though I'm aware of at least one library in Australia (Canberra) that also offers some titles in mobi format. Note that ADE pdf is distinct from regular pdf.
Kindles natively read azw/topaz and mobi books. All other e-ink readers natively read epub and ADE pdf.
Personally, I borrow extensively from the library and based on that, chose a Sony PRS-300. At the time of purchase, there were no e-ink devices being sold at reasonable retail price in Australia, and I bought mine while on holiday in the US. (150USD vs 450AUD when 1AUD=0.90USD) I ruled out Kindle due to library borrowing and Nook due to US-centricism. Kobo wasn't yet widespread. I considered Pocketbook, but the price difference and difficulty obtaining one (having it posted somewhere vs picking one up in-store) gave the edge to Sony.
I download free Amazon books and read them on my PC. At some stage I will get around to converting them for my Sony.
Of course if you have the time, skills and inclination, you can choose whatever device you want and convert books to whatever format you like. Personally, I read in excess of 100 books a year and really cannot be bothered converting when I can simply choose a device that doesn't require it.
Other factors you will need to consider are: price, connectivity (wifi/3g/none - sideload by usb only), touch (or not), screen size, dictionaries and a host of other features. Some or all of these may be irrelevant to you. Note that if you are borrowing from the library you *must* sideload those through your computer. Generally connectivity on a device is primarily for instant purchasing from the related bookshop.
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