This might be a long shot. I came across this looking for something similar, but for ebooks. You may want to download/evaluate it. Apparently the organizing system that it comes with is locked in, but you can add your own folders. It's mostly a front end for VitalSource's ebook outfit, but it's also geared for note-taking, highlighting, reading, etc.
http://www.vitalsource.com/index/bookshelf