I'm a prof now, but I got that way by taking a lot of classes and a LOT of notes. I'll tell you why I prefer to take notes on paper, and then, I'll tell you the most important thing you can do to make sure your notes are effective.

In favor of paper:

-Something cognitive happens when you put pen to paper. I find because I can't write as fast as I type, I have to rephrase and synthesize what the speaker is saying. And to do that, I have to understand it. And when I understand it, I own it.

-If you're taking notes from something you're reading, you will probably type WAY too much stuff if you use the computer. Instead, try this: Read the section or chapter, then close the book and write what you remember. (You may have to start off with relatively small sections at first, until you get used it). It changes the way you read from passive to active. And it will change your life.

-As others have mentioned, you can easily do diagrams and other graphic stuff with pen and paper; not so easily on the computer. Many times spider outlines, columns, arrows, and circles are the quickest, most elegant, effective way to record ideas and relationships among bits of info. Stars, underlining, circling, wavy lines - all these help you graphically construct the information in ways that will help you understand and retain it.

-My mother says, "Once written is twice learned"

-As a historian I've spent lots of quality time with 350-year-old documents written on, you guessed it, paper. Paper does not require electricity and its battery does not die. (And it's easy to borrow, as are pens). Paper can survive war, riots, insects, rain, mold, dirt, dust, and yes, coffee. I once dropped Eric Wolff's Europe and the People Without History into the bathtub and with the help of my blow-dryer it recovered nicely. I love my PowerBook but it's not coming into the bathroom with me. If you think you might study where liquids will be present, or if your univ. insists on holding classes even on rainy days, paper is a good choice.

Now: the most important thing to do: GO BACK OVER YOUR NOTES WITHIN 24 HOURS OF WRITING THEM.
You will find you remember all kinds of things you didn't have time to write down, which you can add. If you wait more than a day, most of that info effectively disappears. Going back over the notes promptly is the single most important thing you can do to help yourself learn and retain information.