PDF Annotator is one of those pieces of software that should be installed in any UMPC or Tablet PC. This easy to use program allows you to take notes on top of any existent PDF file and save your notes with it.
I can write 1000s of words here explaining how easy is that but you never will get it better than watching this short video:
PD: I like the music on this video. It's by Richard H Bright.