Is there a PDF (or epub) reader that allows to take notes (or at least to copy text)?
RepliGo Reader ($5) allows you to copy text and to make annotations.

Also, if you convert them to epubs the Nook app allows you to make notes.  It may let you copy text on a non-DRM'd book but I don't have any of those so I'm not able to test it.  (Just note that while the Nook lets you read PDFs the Nook app currently doesnt.