I’ve discovered that Zim is a great little brainstorming tool, for me at least. While I occasionally “think in images”, my brain usually works on words and symbols. A wiki – especially one that sports a LaTeX equation editor – seems to be a powerful way to assist a text-based brainstorming session. Being a desktop application (rather than a web application), Zim is also very simple to set up and use.
I spent today and yesterday using it to construct some arcane maths involving matrix multiplication. Said maths mostly turned out to be wrong, of course, but that’s all part of the process.