Most of the profs in my school use powerpoint slides to do their presentation. You just download the powerpoint slide from the course/prof website and add in comments to whichever slide you think need it...
My university tuition has a laptop lease built into it, so the laptop pretty well travels to most of my classes with me.
I find that taking notes in Word makes the most sense, even when I have the powerpoints ahead of time. When taking notes in powerpoint, I find that the notes, by themselves, don't have context, and I can't study notes off of a computer screen.
I'm averaging 2000 words a lecture in my Western Civ class, so it serves me well.
For Macs, I've found that the Notes function in Entourage (MS's Mac version of Outlook) works very well. It's easy to use and easy to organize - especially since Entourage has light project management features that you can organize notes, email and calendar entries with.
Pages in iWork is also very good for just random note-taking.