Well there's a place here in Asheville that's pretty hole-ion-the-wall but atleast it sometimes has a better selection than the chain stores. Although in terms of hardware and stuff they're not too well equipped but atleast they sometimes have interesting fish.
And if you're anywhere near Charleston I just stopped in at an awesome one on the way home and picked up 3 baby jaguar cichlids. They've got lots of really neat stuff (they had sea horses, too cool!)