When I went through school, I found that handwriting with note paper and pen was a mixed bag: the act of writing things down helped me learn (muscle memory, as it were) but it also kept me always lagging behind by a few minutes. The prof would be talking about something new and I would be struggling to listen to what he was explaining while also simultaneously trying to catch up on a backlog of notes that I had to have written down before he changed the acetate or erased the blackboard.
At one point everyone started using PowerPoint but I found that also to be a mixed bag for different reasons! Since all the slides were there already it was tempting to not take (m)any notes or even not pay attention at all ("well, I can just look at the slides later"). Having the slides given to you (printed or downloaded) made it too easy to assume you've got it covered. On the other hand, it allowed me to focus on the professor and what was being talked about.
I think ultimately it depends on the subject. Any subject that relies heavily on math and/or diagrams (such as math, physics, music, or a UML modelling class) I would take notes with a pen and paper. A subject that is more suited to taking actual "notes" (literature, social sciences, etc.) I might be tempted to bring a small laptop.
I have taken short notes at a seminar with my iPad before. It can work, but it's not very fun.