Note taking programs are always interesting to try out because note taking is such a personal thing and every user is a little bit different in how they approach the task of writing notes. My program of choice is OneNote but there are several other options out there that are quite good, too. EverNote and GoBinder are very good programs that users swear by and are especially good on the Tablet PC.
I was recently directed to a new entrant in the note taking arena, LivePad from Seeplain. LivePad approaches the note taking problem from a different angle than the other programs and has a lot of ink utilities integrated into the main interface. The program offers a lot of data capture tools making it a real research utility. The program has a free trial available and is currently priced $50.