I'm actually kind of haphazard in my note taking. I use several progams depending on what makes the most sense for the information and the try to store them all in the same place.

However I did come across a program that has gotten a lot of praise you might want to take a look at. It's called EverNote. There's a free and a professional version. I've never used it myself, but I came across it in an issue of PC World awhile back and they gave it a very good recommendation.

I'm actually glad you started this thread since it reminded me about the program.