© 2009 Flying Meat Inc.
VoodooPad is great at just organizing lots of disparate, related information. When you a create a new VoodooPad file, you’re essentially starting a new Wikipedia. You dump info in. Linking is extremely easy.
A great little built-in piece of Ubuntu is TomBoy which is intended as a Note-taking utility. It's not as full-featured as VoodooPad certainly, but the basics are there with the ability to essentially dump a wiki from your brain.