I've been taking notes in LaTeX and keeping them in source control recently. I still prefer to take notes during lectures by hand, but usually within a week of a lecture I'll transcribe them into TeX. It takes a lot of extra time, but taking notes twice like this helps me remember the material better so I don't have to cram before exams.

All the notes I've taken so far are at https://github.com/xjtian/class_notes. There's some cleanup/updating I've been meaning to do for a while but I haven't gotten around to it (summer).