In the Philadelphia area:
Barclay Prime
Black Sheep
The Bards
Copabanana
Good Dog Bar (try the one stuffed with blue cheese)
London Grill (on an English muffin, no less)
Rouge
Although it doesn't make this list, I like 5 Guys, but understand Unsound's criticism.
Of course, if you come here on a visit, skip the burgers, as you can get them in any city. Try the hoagies (subs to the rest of you), roast pork, roast beef, and cheesesteaks.