Personally, I also tend to start with a text description of what I want the script to do which I then break down until I end up with a mix of pseudo code and comments, but in the past I've also created flow-chart type things.

I never used a program to do it, just a large dry erase board, a marker, and some larger sized post-its.

Its simple to use and takes almost no time at all to get started. I can move things around quickly, draw/redraw lines between notes, stack notes on top of other ones, or replace notes all together.

I think if I had used some kind of visio-type program I would have spent all my time playing with different boxes/borders/fonts/colors or at least spent time learning the ins and outs of the software itself when what I really wanted was to get to work solving the problem at hand.