I've heard quite a few genealogists mention using the Evernote program to organize their research. I downloaded the program awhile back, but it wasn't until just recently that I've started learning how to use it.
It seemed rather confusing at first, until I realized that the layout is quite simple: the key for me was to see a "note" as sheet of paper, which can then go into a notebook. Then you can have multiple notebooks, organized into stacks. You can title each note, each notebook, and even each stack.
So far, I have one notebook for genealogy contacts, and another for tasks.
I think there are some more techie things you can do as well, like having emails pertaining to your research automatically added to Evernote and sharing your notes/notebooks with others.
Will have to play around with it some more this weekend.