In running my 4e campaign, I use DnD 4e Combat Manager that I found here on the boards. It's a great, simple little utility that keeps everything I need for running combat.
I also frequently use music during games (and less often, sound effects). I've tried a few different programs, although I'm really liking RPG Atmosphere lately.
I've been incorporating OneNote into more of my campaign note taking and tracking as well. That's typically after the session, however.