FreeMind is free Mind Mapping software that works on most platforms. It has cool feature where it can create navigable map of your file structure. The .mm files are XML so one should be able to do other sorts of transformations on them.
Here is a sample .mm file:
<map version="0.7.1">
<node TEXT="What is MindMapping?">
<icon BUILTIN="help"/>
<node TEXT="A technique of brainstorming" POSITION="right"/>
<node TEXT="A type of software to help thinking" POSITION="right"/>
<node TEXT="A type of hypertext editor" POSITION="right"/>
</node>
</map>
James Chartrand sent me a link for another free Mind Mapping tool, MyMind 1.2 – I haven’t tried it as it is only for Mac OS X 10.3.