I've bought from Shortcovers - good experience. 7 or 8 books now, plus a whack of free stuff. Got won over when they added Adobe Digital Editions/epub support and started matching Kindle on bestseller prices. Been smooth so far (after some early fights between ADE and Snow Leopard, which took a little head-scratching to sort out. their customer service rocked, even though it wasn't their problem.) Now I'm moving books over to an "old" Sony PRS-505 for reading during the day-time, and reading the same book on my iPhone in bed (no reading light needed - a bonus for the significant-other.) And the iPhone doesn't count for the "no more than 6 devices" ADE rule, which is a nice bonus.
Haven't tried Calibre. Just using ADE to move stuff to the Sony. The Sony software still bites, but at least it's on the mac now.
As for your future-proofing question: Yep -- you end up with an Adobe ePUB on your machine. If you drop Sony and get something else that supports Digital Editions (which most of the non-Kindle readers do), you're off to the races. And Shortcovers has other mobile platforms too, so if you end up with a Blackberry from work or something, you're still good to go.
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