In addition to Tufts Universities' Visual Understanding Environment (VUE), I also discovered CmapTools. It appears a bit older than VUE, but in some ways is more functional. Like VUE, it provides a means of building concept maps. Concept maps are like mind maps, except that they do not have to have a central node. See concept maps on Wikipedia for more information.
I am very interested in expressing concept maps semantically so that they are machine readable. This could make the information useful for other purposes such as other visualizations. For example, see my previous post, "Network Visualization Within Diaspora (cont.)". As usual, the bioinformatics community seems to be ahead of the game. See a website on Semantic Maps for Bioinformatics.