This is an issue I have personally grappled with a lot and I think that it depends on what you are learning.
For example, I was an engineering student who faithfully took all my notes on paper with pencil. It was easier than computer due to having tons of equations, graphs, diagrams, etc which could not be conveyed to a keyboard so easily.
When I started med school, I was so used to the paper and pen model, I didn't see the need to use a netbook. Big mistake. The information they present in med school is BIG on volume, and I could not keep up with class. I found that after switching to netbook w/onenote, life improved by a lot. If I could type faster than the professor spoke, I had time to think about things.
I miss not being able to copy down graphs, etc but frankly the CT scans and cells they show in here could never be conveyed to paper anyway, they are easier to copy+paste from professor's slides into one note for later review.
The best medium of notetaking really depends on what you're doing. IMO.