I have finally started using a mind-mapping tool, Kdissert, and I have to say, it's pretty cool. Mindmapping tools are great for organizing many related ideas so you can map out what's what.
The other thing is that mind-maps can look kinda snazzy. In Kdissert, by default, it draws straight lines from one idea to another. However, you can make it draw splines instead and then the ideas look like they're being grappled by tentacles, it's really cool. Here's a mindmap I'm working on, apparently, my mind looks like the coming of Cthulhu:
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