a brain to think up things, a notebook and pencil to write them down.
The best ideas come in bed, in the car, in the train, while hiking the woods, in all the places you just don't have a computer ready.
Besides, picking up pencil and notebook is a lot quicker than booting up a laptop, starting VI or Word, finding and opening the file to edit, editing it, and closing everything down again.
I use a little green notebook and MS Word. As you can imagine it's very cumbersome. A great deal of my time is spent designing xml schemas, and, well, neither is what I would call suitable for the job.
I have never actually tried any software tool designed to do this for me.