Since I'm writing fantasy novels, a map (or in this case a series of maps) is essential. For each map I make, I use Photoshop and Illustrator. More recently I purchased Campaign Cartographer, which specializes in making maps for role-playing games. I bought this application to see if it was be an improvement over Photoshop and it is. But I can't import the maps I've got easily and redrawing them will be too much work. However, if you are starting from scratch, Campaign Cartographer might be a big win for you.
Likewise, I mapped my entire fantasy world some years ago. If I were started from scratch I probably wouldn't do that. I'd use Fractal Terrains. The nice thing about that program is it integrates with Campaign Cartographer I believe, and will randomly generate the entire world in a snap.
I also spent a lot of time doing research on magical components, plants, metals, animal parts, used in alchemy and spells. I collected the information in a database. I was using FileMaker for this, but have moved over to Bento because it integrates with my smartphone, making it easier to look up information when I need to.
Other tools to consider: name generators, town generators, and other vertical-market role-playing software. These can be a real time saver when all you want to do is write and not be bogged down by the details. This happens to me when I've got a great idea and want to capture it. I'm often writing so fast I don't care what the minor characters are called because I can always change this later.
And that's the majority of the other software tools I use. Of course, if I find more I will share.