I have a franchise customer who is looking to reel back in several "rogue" franchisees who did set up their own domains, like www.[franchise][location].com.  The problem is that, as I think was mentioned here, those local sites are ranking higher than the "fully optimized" main site with the location sub-folders.  Now having to go back and require 301 redirects is an absolute nightmare, particularly when you're at 100+ locations.

Has anyone done a successful migration away from multiple sites into a single root domain?

This is a great point, Scott.  I wonder though if you couldn't use the zip code feature in Adwords to create unique campaigns for each store location, even in the same market, and then drive each ad to their respective location page on the root domain.  Would this work?