I have a feeling this article from Lifehacker on converting PDFs to ePub and other ereader formats will come in handy soon. Lifehacker recommends downloading and installing Calibre e-book manager which is a free program to convert over and edit the meta data for your PDF eBooks. With Calibre you can covert non DRM PDF files into the ePub format that iTunes recognizes and sync them. If I'm not mistaken the Kindle software also uses the ePub format.
Currently there are only a few eBooks that I own that I'd like to convert, including my 2010 PADI Instructor Manual.