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The question isn't so much one of formats -- though PDF does have the major flaw of being intended to exactly reproduce a page on the same size paper it was laid up on, which is great for tax forms and terrible for ebooks -- as it is of DRM. If your ebooks are DRM-free, you can convert them into whatever format your reader happens to use (I like calibre for that purpose -- it's supported a few forums down) or, for that matter, whatever format the ebook reader you buy two years from now uses that hasn't been invented yet. If your books are DRM-restricted, then you're stuck with whatever the book vendor wants you to use, and if you upgrade to a different reader, you have to buy the same books all over again. Or strip the DRM, which we can't talk about on MR.
I'm one of the epub partisans, because I've got a Sony Reader; people who have Kindles use mobi, and while they're pretty much the only people who do, there are a lot of them. And, as ATDrake said, there are all sorts of legacy and niche formats out there, too. That's why freedom from DRM is so important.
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