I just use MS Word. Sometimes I take notes by hand and then later convert them into word and organize/try to make sense of them. It really helps me lock them in that way.
Sounds like that certainly works for you.
What's really coming across in this thread is that there are many ways to go about taking good notes in class, and the original question therefore has myriad possible answers. Even what constitutes "good notes" will vary--in a science course, your notes might well be full of concepts and terms you'll need to memorise. In maths, taking notes by hand may be the most practical solution. In a history course, the whole lecture may just be summarising material you should already know from the reading, so taking notes becomes just about taking down anything that's new. The applications that suit those tasks and those styles of taking notes may differ. I will say, though, that I cannot understand why anyone should think it at all important that the application used for taking notes
look like a "real" paper notebook.
Some people swear by taking notes by hand. Personally, I've tried it both ways and discovered that I take far more comprehensive (and organised!) notes if I take my iBook to class (I type faster than I write, and typing seems to require less concentration). There's just no comparison for me. And the last thing I want to think about when I get home after a long day at university is having to type up notes I took by hand. So it's VoodooPad for me, and I never lose a page of notes, and I can drag in handouts and such once they're posted in the university's online education system so they're right there in the file with my notes for that day, and I can export my notes to my iPod with two clicks and sit reviewing all my notes while I wait for a lecture theatre to empty out so I can go in ...
But clearly, everyone's different. My advice to the OP is to try out a number of the applications people have been recommending--there is no "best" notetaking app, only one that's best for you. See what works for you. I'll just add "Mori", from Apokalypse Software, to the list. It didn't fit at all well with my notetaking style, so I switched to VoodooPad, but that's no reason it won't work for you!
