I'd never really seriously considered mind mapping software, and while I still don't think it's exactly what I want, it actually seems to have more potential than it seemed. Thanks for the suggestion.
For tree data you may want to look into various XML designers / editors. You can easily define a recursive XSL style sheet that has the structure you want, after that there are various editors that automatically read that structure and give you a GUI from it.
It's been a few years but I found XMLSpy to be fairly decent. http://www.altova.com/xmlspy.html
Edit: The simplest tree editor is probably the file system on your computer. However, the problem is for proof's I suspect your going to want to have some sort of graph structure.
PS: If your willing to do some light coding XQuery/XSL-FO let's you transform the raw XML into various more user friendly formats like PDF's. However, if your structure is really nested that quickly get's hard for people to understand.
The issue with a lot of mind-mapping software is that the data must be strictly hierarchical. Sometimes when brainstorming you want to represent data with cross-links or in multiple categories, which is where something like Graphviz, Instaviz, Omnigraffle or Visio come in.
