When I was in college I more or less tried a different note-taking system every semester.
I tried just writing things down free-form, making flashcards while I was in the lecture, drawing mind maps, drawing one continuous mind map that would be compressed over the weeks of the class.
They all had benefits and draw backs. Flash cards were kind of fiddly and distracting to make. Freeform notes were slightly disorganised.
Whatever I did, I found it helps. For note taking, the act of taking notes is more important than what remains at the end. Be honest, how often do you really go over your notes?
For things you absolutely have to know, I really do recommend flashcards. That said, I think they are quite difficult to produce when you are are learning something new. Flashcards aren't really for learning, they are for not forgetting.