I have been using Freeplane, a mindmapping program, for a long time to organize large amounts of information. I can semantically organize literally everything there is to know, so that I can make connections, eliminate redundancies (very common in social science!), and try to develop new knowledge. I can't say enough about how much I love mindmaps.
If you're not familiar with mindmaps, they're basically concept maps that allow for very rapid data entry. They focus less on the artsy crap and give you keyboard shortcuts to get your ideas down extremely quickly.
I'm just now getting into programming and Mathematica. The Wolfram products have all sorts of in-built abilities to create visuals of data; are mindmaps one of those visuals? This could go for Mathematica or any other product made by Wolfram.