(I don't claim to be using my notes to any great effect, but this is what I do with them):

To me, I've noticed that I seldom actually use my notes as a reference. When I need to refer to something, I go to a place in a book somewhere. Rather, during a lecture, my notebook for the class seems to function more as a way to keep me paying attention to the lecturer, and to run various complicated pieces of information (equations, etc) across my mind. (Okay, I do sort of refer to these during exam study, but the books tend to be more legible).

I also do a lot of my own investigating of various subjects. I will be reading a book, and noting the equations, then go off on a tangent playing with the equations, or attempt to re-derive something that I may or may not have played with before. I have several 5-subject spiral bound math notebooks that I will fill with whatever ideas I am currently playing with. I try to expend one of these every 3 months or so, though my current one is 5 months old. :'/

When I am done, I clip the spiral binding and roll it out of the notebook, then use my document scanner to scan the thing and put it in my notebook library for future reference. (Some of it I do end up looking back to, but hardly most of it,.)