The idea of optimizing a graph layout based on the subject matter that its modeling is a really interesting idea. I'm in the camp of always interested in more visual programming techniques / aids, so it would be really great for us to be able to visualize something as complex as a large program this way.
I've used dot+graphviz to visualize algorithms and data structures before. The syntax makes it really easy to get started with, just print out "x -> y;" in your inner loop or whatever.
