convert your paper notes to xournal
 

I like Xournal very much. And now for yet another reason: because it is quite easy to convert your handwritten paper notes to the xournal xoj format (and then edit, annotate, convert to pdf as wished).

Get here the script for your linux box to convert scanned notes to xoj. Some dependencies are needed - they're in ubuntu - debian repositories though.

Another script to combine several xoj files into one is also included.