This was my first thought as well. I use graphviz quite a lot for these sorts of diagrams, and I really like it. Their site, reference materials, etc. need updating though.
There's an interesting art to knowing when neato or twopi are better choices than dot for layout rendering. Graphviz is interesting because there are multiple layout renderers and "non-ugly" is a graph-by-graph art form between the different renderers and different renderer hints in the graph file (spring constants and what-have-you).
I've had some successes and a lot of failures over the years.