Currently college senior and successful note-taker here. I was a Windows user and I am currently running Ubuntu 7.04, but the advice I am giving is platform independent. In the past, I ran a personal wiki (multiple in fact), specialty note-taking software, and even pen and paper (good pens, good paper). But I didn't pull it all together, and I more or less lost 2 years of work because of it. If you want to skip how I do things, just read the last paragraph.

My current system is a folder tree, a series of plain text files, and Google Docs.

I created a folder for each of my classes, and in each of the folders created a file with the name "CLASSNAME"_notes. I take all my notes for that class in a single text file. At the start of each class I fire up my text editor and sign it with the date. I do not fret formatting, colors, font sizes, spelling, or really anything besides data dumping. If the prof supplies another material for the class I put it in the same folder (PS even if a prof gives you something on paper, ask for it electronically. I have a 100% rate of return on that question). After class, I go back over my notes and make them look nicer and reprocess them.

I use Google Docs whenever I need to share material with anyone. Study groups have never been the same since everyone could be working on the same guide from either a remote location or a physical group.

I would highly encourage you to not dabble as some have suggested, and certainly do not actually buy any software (being a college student is being thrifty right?). I would recommend that you relisten to Merlin's Podcast titled "It's Just a Cup". Your system is just a way to Get Things Done - it doesn't need to obey your every whim - it needs to gather data so you can reprocess it later, and do so in a way that you don't need to think about it. In other words - if the choice is to go simple and quick or complex and powerful - simple and quick win every time. Your ability to take notes is exactly that - your ability. No magical piece of software is going to make you better at that. Thinking otherwise is simply deluding yourself into a false reality.