Hi
I'm with Hazyjane on this one, printing & lots of scribbling/annotation works well if you like the solid nature of a piece of paper in your hand. It's easy enough to make notes on papers to make links to other literature, then I've put all mine into separate folders by subject & ranked them in the folder - good ones at the front, poor stuff further back, really poor stuff in the recycling!
Having good notes obviously makes life easier when it comes to writing up too; then reading & re-reading, reading, reading some more...
Good luck!
Mog