Just remember that some books will have to be scanned manually, probably into TIF/PDF, anyway. Xournal seems to be a good option, and PDF is more portable (or "cross-platform") than OneNote (suggested
here) and Windows Journal.
BTW, have you tried Jarnal or Gournal...?
Cheers.
P.S. Ahh... Forgot that while PDF are readable on most platforms, the notes taken with Xournal cannot. Good thing is that discussion about this has happened on Xournal-devel. Maybe we'll see one released later.