Both the Kindle and iBooks apps have built in notes taking ability. Neither are the greatest, having several restrictions to keep the paranoid book publishers happy, but they are more or less usable.
Most ePub, iBooks will let you email/share a note. Combined with Evernote (which provides an email address to add notes) you could do a pretty good job of collecting and organizing them. Here is a couple of samples showing what the Evernote solution does. One with an iBooks Textbook, and the other with an imported (not from the iBooks Store) ePub. That's the two extremes. No notes for PDF files, btw. There are better apps for that.
I don't see anyway to export notes directly from the Kindle app, but I believe you can do so from the Amazon site. Never tried it though, so no promises.