[clayasaurus]

http://freemind.sourceforge.net/wiki/index.php/Main_Page

Let's you map out all the ideas for your game on a tree, and export it to cool formats. A great tool for organizing ideas. I use it for trying to think of every possible feature to be implemented into my game, the levels, the setup of a level, the menu, etc. Once the mind map is complete, it gives a really good solid foundation to start coding with.

I'd suppose this would work well for any large software projects.