[FlorenceArt]

MarginNotes handles both PDF and ePub. Not sure it could be a one stop shop though, it's not as refined as Marvin and still needs some work (it has improved a lot in the few weeks I've known about it though). I use it for non fiction books, where I am likely to take a lot of notes and the book itself has notes. MarginNotes displays them in the margin, as the name implies, and that's very useful.

For fiction I have switched recently to Marvin and am finding it very good. As for fiction PDFs, I'm afraid I treat them much like paper books. I occasionally buy or download one, but somehow I never get around to reading them.