Philadelphia has a few - Firehouse in west philly and Via in south philly.
Used bikes tend to be pricey - but they somehow make a go of it and folks buy $300 varsities. Both locations are in old, established buildings - so maybe lower overhead helps. On the repair and parts side - it's helpful to have them around.

http://www.firehousebicycles.com/
http://www.bikeville.com/frames.html