You may be very interested in a document I came across a while ago, which is one man's manifesto on note-taking that he compiled in a (free) ebook called "How to Make a Complete Map of Every Thought You Think." You can find it here: http://www.speakeasy.org/~lion/nb/

The program he sets forth is extreme, as he is quite literally trying to detail and commit to memory (on paper) his entire mind. But it contains a lot of useful advice on how to take notes that are useful, accessible, and memorable. I've implemented bits of his system and it has helped a lot in school - I've found that it's much easier and more useful to take notes when there is some method to the madness.

Oh, and if you are at all a visual thinker, Always take notes on paper. Paper offers freedom that lines of computer text simply can not: arrows, diagrams, color of pen, relative sizing of text corresponding to its importance, arrangement of elements on the page, all of these things are immediate, intuitive, and completely your own. I'll cite a paper that highlights the importance of this sort of visual language: http://www.stanford.edu/~rhorn/a/recent/artclNSFVisualLangv.pdf