I've used GraphViz to render the relationships between three layers of data structures in a system integration (system A, wire format, system B). I had to reconfigure the layout engine to sort the structures into ranks, and lock their spacing far enough apart to make room for the dozens of edges between nodes. I also used the pseudo-HTML node layout syntax, and spent some time working on styles and a color scheme.

So it wasn't automatic, but the resulting diagrams were beautiful, illustrative, and informative. Before that nobody on the team had fully acknowledged the complexity of what we were undertaking. I showed, with the help of GraphVis, both that this was a complex integration, and that it was possible to untangle the complexity.