Lifehack.org suggests that students use wikis for course note-taking. The article drops names for some basic wiki software — NoteMesh, stud.icio.us, and PBwiki — and includes a helpful brief guide to wikis and their care and feeding. [Side note: I tried entering in my college at stud.icio.us and got an "Application Error" message, which isn't a good sign.]
I’d add Wikispaces to that list — I’ve done two wikis using this service and found it to be very good. And I believe it’s the only free wiki service with LaTeX support, which makes it especially useful for math classes. (If you know LaTeX, that is; if you don’t, I have some screencasts for you!)
All of these services are web-based. That’s good if you want to collaborate with others asynchronously or if you need to access your wiki from different internet-connected machines. But it’s not good if you’re not always connected to the net or if you don’t want to have to factor in the strength/speed of your connection into the usability equation. I’m in this latter camp, and so for my offline-wiki needs I’ve been using VoodooPad Lite for designing my fall courses — which is sort of like note-taking. It’s been a very good tool for this purpose; I just dump whatever comes to mind into a new wiki page and the links to existing pages are created automatically. VoodooPad Lite is free, but it’s Mac-only. (Anybody know any Windows or Linux offline wiki software for the rest of the population?)
There’s a real value in this kind of non-linear information processing that could benefit a lot of students whose brains don’t fit well with bullet-pointed outlines.