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You're confusing formats and stores.
Some devices whose sellers are trying to tie them to their company ebookstores have "official" formats.The Kindle, for instance, uses azw, which is a slightly tweaked mobi. The Sony Reader uses epub (used to be lrf). I'm not even sure what the Nook uses -- epub, isn't it? (Don't quote me on that). Others whose sellers are not also selling ebooks are store-agnostic, and can display any format they support, DRM permitting of course. Independent ebookstores (Smashwords, for instance, or Webscriptions) supply ebooks in a variety of different formats, particularly epub, which can be read by most ebook readers.
So what you need to be concerned with is platform lock-in, DRM, and compatibility. One big question is how these ebooks are going to be used, and on what device(s). If you tell me that, I might be able to toss some actually useful advice in your general direction, instead of nattering on about formats.
(and yes, I'm using file extensions as shorthand for their formats; I'm lazy and my finger hurts where I skinned it on a particularly ferocious bucket)
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