I wrote a program called PACT (Posterior Analysis of Coalescent Trees) this spring to properly analyze the genealogical trees produced by Migrate. I finally put in the extra effort to write documentation and make it easy for other people to use the software. Source code is available for download.
I had originally wanted to estimate the relative contribution of various geographic regions to the evolution of the influenza virus. Trees produced by Migrate contain an explicit description of which geographic region branches reside in. It was just a matter a extracting, displaying and summarizing this information. The program can do a variety of things beyond this, and hopefully should prove a useful accessory to any sort of coalescent inference.