I've tried all different ways to take notes during college. What I've finally settled with is using binders to keep track of all my handouts/papers and to do practice problems in. For taking notes, I use my computer and put the notes in separate folders according to subject.
Just because you have to carry a binder around doesn't mean it can't be cute! Also, by organizing a little bit, you can make your binders functional to fit your needs. Here are some of my binder tips:

Binder Tips by preppypremed on Polyvore
A little more explanation:
1. I have a binder for my M/W/F and T/Th classes. That way I'm (hopefully) only carrying around one binder per day. Maybe at night when I go the library I'll have to bring both with me, but two binders is pretty light considering I used to make a binder for each subject.
2. I use binder dividers such as these to divide the binders into a sections for each class. In each section I put a folder and filter paper.
3. I make a LOT of notecards to study for quizzes and tests, so I need a way to store them. I use a pencil pouch inside the binders to store notecards. Otherwise I lose so many notecards inside of my backpack.
4. Finally, I personalize the front of my binders by printing out pics from the internet or making a picture collage. This year, I followed The Pink and Green Prep's tutorial to make the following binders:
What do you all think? Do you have any tips for school organization?