When I posted about barbarians at the gates last month, I did not expect the most famous one in English literature to appear in response. As it turns out, the upcoming Age of Conan has exactly what I was looking for, including PvE and PvP city-building and -defense that integrates crafting and has various sizes for big and small guilds. Ask, and the internet delivers.
My thanks to our commenters who pointed out my ignorance and cited other games doing something along these lines. Please consider this your report-out on games that have aspects of player-run, -built, or -defended cities. Add more to the comments if you think of any.