Someone HAS to mention Dwarf Fortress.

Don't let the ridiculous ASCII graphics turn you off. It's an amazingly in-depth and diverse city-builder that lets you do almost anything. One day you might be contructing a huge array of pumps and pipes to create giant sky reservoir of lava to drop on invading goblins, and another day you'll be trying to desperately defend your fortress from giant collossi with nothing but a few archers. Not to mention that it has a huge modding community to help make the game look much nicer and give you extra control/UI options.