This recent discussion post by SarahC got me thinking about how one can rationally manage research. It seems like software might be useful here, but I don't know how exactly the software should work. I'm intrigued by mind mapping software, but it's possible that all that structure is unnecessary and you could do quite well with less. For instance, I'm considering trying a system of timestamped notes which are managed by a tagging system. If the tagging was done thoroughly enough, you could filter through all the posts sharing a cluster of tags and fairly easily get access to every idea you've recorded on a certain topic.
The only problem is, I think I'd want even more specialized software than that. I'd want to integrate my notes with some form of bibliography management, and at least a to-do list. And I can imagine more, for example perhaps there could be a "sticky note" capability where I could pin up and move around things that I either want to remember or that will help me with my research, like an inspirational quote if I'm not feeling motivated to do research, or the Litany of Tarski or some other rationality technique if I really need to remember to use it.
I'm not sure if these ideas are all sound, but a basic requirement for the software would be to document the structure of your research so that it can be analyzed for effectiveness.
I know there are some people on Less Wrong who do research, so I suppose I should defer to the experts here: how do you organize your research? What methodologies and tools do you use? Why?