Performancing has an introduction to Using Mindmaps: 5 Steps to Letting Your Blog Posts Write Themselves. The article is about writing blog posts, but you can use mindmaps to organize your thoughts about anything. I used a mindmap to get my thoughts organized when I initially started working on my dissertation. It’s helpful, because you can diagram the relationship between different ideas without forcing them into a linear sequence. For a good introduction to mindmaps, see the wikipedia article. I am using the open source program Freemind to create my mind maps. If you’ve ever been frustrated with having to force your thoughts into a linear outline, you might give it a try. Unfortunately, when you write the paper you eventually do need to put your thoughts into a linear sequence, but at least you can be freed from that constraint during the planning phase.