What is your favorite application of Graphviz?
makecheck: I use it indirectly from Doxygen regularly.  I've also had data in custom formats that is naturally graph-like, and it was trivial to produce visualizers by writing scripts to convert the custom format into "dot" syntax.One idea I have is to use "dot" to give auto-layout capabilities to a GUI that has a simple canvas.  Right now, any data set that wasn't created by a GUI user (e.g. automatically generated) looks ugly, because it has no useful layout information.  Since "dot" knows how to do layout, it would seem possible to run it in the background, parse the results, and use the node positions to make the default canvas look much more intelligent.