I have always been a fan of the MS office for notes, although I'm trying out pages now.
I create a new section, and use the date of the class/research as the header. I can easily scroll down to what date I need to go back to. Search for anything, etc.
I generally take notes by hand, then transfer them to my computer. My profs/university realize most people are surfing the net/facebooking the entire class period so they often don't allow computers in class.
I can't verify if this is true or just a coincidence, but most of the class rooms don't even have wifi anymore. When I first started going to college in '05, every room had wi-fi. When I transferred and started to work on my second degree, the buildings had wifi, but the individual classrooms didn't. Perfect reception in the hall, minimal to no reception in classrooms.