Hi adamschoales, I'm also a college student and last year (my freshman year) I came across the same dilemma. I guess I'll share the methods that worked for me. If the teacher actually gives you any files, for example the powerpoint/presentation used by the teacher during class, I would take notes on that. Especially in that case, having the extra notes coupled with the presentation will allow for you to easily follow the mental process of the presentation and remember things for later. For classes without actual files I am a huge advocate of simplicity on this. Merlin and wood.tang have it right, paper and text files are where its at. Much like the GTD "Inbox", it doesn't matter what you use to collect your inputs, just that it works for you. Also, like I believe either Merlin or David Allen said, it should be something with the least amount of interference. Wood.tang is right that the screen is a wall, or better yet a window to all the other things you could do (internet,etc) which keeps you from concentrating.

The truth is, you are supposed to concentrate on the information in the notes not the program/media its on, so the notes should be well named or organized in places you can find them easily. Getting fancy with pictures and links sounds nice, but in reality it only distracts you from the information at hand. In the time it takes to make a word a special color, or attach a picture, you probably missed something important the professor just said. Choose the path of least interference between brain and storage, and you shall prosper. Oh...and study them. Notes don't help if they remain un-read. Good Luck!