I would use pen because of the permanency (sp?), and in a one of those spiral binders which already has the line paper attached to the binder. And if you have handouts, put it in the open pockets that come attached to these binders.
take notes on your laptop. who the f**ck handwrites? and if you insist on handwriting, who cares if you use pen or pencil? use whatever you used in undergrad.
Go to the a forest and find a birch tree. Shave off a 100 ft. long piece of bark for each class you have. Buy a platinum sewing needle. Prick your finger and take notes in blood. If anyone wants a copy of your outlines, demand that they copy it just as you have written it.