I am currently in the process of writing my PhD thesis, and I discovered that relying on a mind mapping software can in fact revealed very useful especially at the beginning of the process. Indeed, I found mind mapping softwares like FreeMind very useful tools to graphically organize ideas into a hierarchy and that allows you to quickly and very efficiently construct and update the outline of your thesis.
It is actually easy to export a mindmap from FreeMind into a hierarchy of latex sections, in order to directly get your document structure ready to fill.
I am actually using this XSLT definition to do so.

The only problem when working like this is that once you have exported your document structure from Freemind into latex, you have made modifications and written some sections into your latex, there is no way to import it back to FreeMind in order to reorganize your document.

To allow this usage, I wrote a small groovy script for FreeMind that read a latex file and build the tree hierarchy out of it. It also imports the content of the sections into the text attribute of the nodes, and this content gets correctly exported by the latex export XSLT.

This script must put into the FreeMind/plugins/script directory, and the following section must be added to the FreeMind/plugins/ScriptingEngine.xml file in order to get the script visible into the Tools menu:

Of course, this code is provided with no warranty, but it should work well :-)
Have fun !