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I'm still waiting on my Nook to arrive, but using Calibre's viewer as a guide, I have found that the best way to handle slightly more complex PDFs (double column, tables) is to use Acrobat to output to HTML and then use Calibre to convert the HTML into an ePub. There will still be some rough patches (especially if it has figures, etc.), but a quick cleanup of the HTML can be done using a free WYSIWYG editor, getting you acceptable results.
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