While Andrew was recently working to develop a new Auto-Retopology routine, based on this recent article:
…there were a number of requests on the forums to “meet in the middle” and allow users to create some guides in the process, that dictate where they wanted the edgeflow and let the program take it from there. It’s looking very promising thus far.
Retopo’ing a Stink Dragon
…and an Orc:
He is working to optimize a few remaining areas, but a new build with this feature should be eminent. They also have a booth at Siggraph, so you should be able to see it demonstrated there, if you’re in the vicinity.