I've become interested in abusing concept mapping (Wikipedia article, explanation by the inventor) as a technique for analyzing the design of moderately large software systems. (The systems are two compilers: One is about 25,000 lines with a 1,000-line runtime system; the other about 200,000 lines with a 90,000-line runtime system. Neither system is written in an object-oriented language or style.) I'm interested in something much simpler than UML; a concept map is essentially a directed graph with just one type of node and one type of edge. I would like to know if there are good software tools for this kind of job; I will upvote any answer that reports on experience with concept-mapping tools.
I'm not particularly interested in generating the concept maps automatically; we've done quite a bit of visualization by automatically generating graphs using dot, and this was useful in its way, but we're looking for something that will enable more control over the layout of the final graph.