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If books are in ePub format and DRM free then they should work without issues in iBooks, Stanza, Bluefire or Quickreader on the iPad (there is a wide choice of eReader apps that can handle ePub). You also have vender specific apps for Kindle (Amazon), Kobo, B&N. The Sony app has, I hear, been rejected.
Calibre has specific integration feature for working with iBooks.
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