Since I don't use a computer at the game table when I run (it just seems like a lot of trouble to me), I put all my GMing notes in notebooks. I may print out some tables or charts or something and keep them seperate so that they're handy, and I'll type up any player handouts due to the fact that my handwriting is illegible.
Creativity-wise, I have trouble making myself sit down and focus at the computer; I'll use it to organize stuff that I already have, but can't seem to get around to making anything new (if that makes sense). Just about all the actual prep-work for my games has been done in front of the TV or something else that I refocus on while I'm thinking. With a computer, my method of refocusing would be either to go do something else, or to start playing games or surfing the net, neither of which leads to getting any work done. I can sometimes get into the flow by juggling different things, switching between Word windows, etc. I guess basically I just like to have something to fall back on while I'm mulling over where to go next.