* Austin, TX (seems to be the obvious pull-ahead winner in 2013)
* Portland, OR (great weather, beautiful, lots of potential)
* Madison, WI (near Chicago, great college town, not as cold as people think)
* Minneapolis, MN (underrated gem, beautiful, just very cold; I'm told they haven't had a 60+ yet in 2013)
* Pittsburgh, PA (CMU is right there; how is it not kicking ass?)
* Ann Arbor, MI (another Midwestern gem)
* Chicago, IL (if you consider that low-COL)
* Toronto, Ontario (ok, not a US city, but I spent a summer there and loved it)
Almost none of these would be considered low-COL (they're above 100) and relative to their regions they're quite high, but they're a hell of a lot cheaper than New York or Palo Alto.
Oh, one ass-kicking advantage of the low-COL places: people actually want to be lifelong software engineers. In New York, you can't raise a family on a (non-WS quant) engineer's salary.
Of course, most of young idiots have this insane dream of having a manager's title and pay (plus real stock options!) which you can get by 27 if you play the politics, but being full-time programmers and just using their magic manager powers to assign themselves the best work. It turns out not to work that way. Poor them...
I really think the fact that one can't raise a family out here on an engineer's salary is toxic to the culture. It creates the wrong kind of ambition.