[mpbm]

I'm working with graphs myself. There's some good research on graph visualization, but most of it is behind paywalls. If you're a student you can probably get in. The hardest part is combining the graph (nodes & links) with labels. I think most people let the graph itself dictate the drawing, which is a mistake. The labels are probably more important, so the layout of the graph should be rectilinear. Visio does a good job of that. Also, it seems more important to layout the graph starting from the node the reader is focused on, rather than layout the whole graph like a static map, because the reader cares about the thing they're looking at and what it's related to most.