I have found a great (and free) note taking program for historians. It is called scribe. I am using it on my long-term projects.
For my dissertation and most of my other work, I've always relied on physical note cards. So that I would handwrite evidence and quotes from books on note cards, or (in later years) type my notes on computer, print them out, and paste them to a physical note card. Once I had my stack of note cards, I would arrange them in an outline and write my paper at the computer with my cards sitting next to me.
What scribe offers is a program that allows you take notes on virtual cards and link them back to a reference source. You can then do fancy searches for certain information on the cards, put them in outline format, make comments on the cards, etc.
I am just at the beginning stage of using this program, but if it turns out to work well on this first project it is going to become my primary research tool. I might even force my student workers to eventually place all my physical note cards on computer. I really do love technology.