It seems to depend on what format is available in their library, but I'm hoping they'll eventually stock epub versions of all of their books. I'd rather get the epub from another bookseller and sideload it than get stuck with only a pdb from B&N. (I know, I'm an epub snob.
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With my library, only two of my books have downloaded to my Nook or the PC software as pdb's. But from the web all of them are pdb's except for the books from Google Books and a newspaper and a magazine.
Actually this arrangement works for me. I have the epub for my Nook and Mac/PC, and the pdb versions work on my Palm Centro using eReader.com's software.