I primarily use Microsoft Excel for HeroForge, SpellForge and my own custom spreadsheet for tracking all sorts of campaign related stuff (that one is for Savage Tide but it's easy to adjust). EDIT: I would like to use Ubuntu but until Heroforge works there I can't make the switch!
I also use PDF995 to create PDF files of stuff I write in Word (like stat blocks, spell cards, etc).
Fantasy related, I use Fantasy Grounds II to run my Thursday night Age of Worms campaign. Things have improved vastly in this latest version. I used to complain about stability in FG1, not so with FG2.
I just purchased Dundjinni recently, but I suck at it. It looks super powerful but I need to invest some time playing with it. Perhaps on vacation this year I will get a chance to work on those maps a bit more.
Oh, and Gimp for image manipulation. It's how I scale maps to tabletop size for use with miniatures.
Right now, nothing. Once I get the system board replaced in my other PC, I'l be using Autorealm, Campaign Sage, and the S&S SRD tools (i.e., the electronic DM screen and die roller).