I go to a local store that's literally named Aquarium. It's big, it's right next to my favorite nerd stop (a giant book store), they will order anything I ask for, and they've got a well qualified staff. I generally only mess with "common" pet stores when they have a sale or I'm interested in a very common fish (corys, tertas, etc).
Petsmart, Aquarium Center, or MsJinkzd on here . I try to avoid the big box stores unless I know exactly what I want and all of it's care requirements.
I've been very impressed with Drs Foster & Smith Liveaquaria (cardinal tetras) and Mellow Aquatics for angelfish and cories. Both do a fantastic job shipping and fish are just gorgeous!
I've got a trio of specialty aquatic stores in my area that have very good variety and carry some uncommon fish, or will order them for you. Huge selections, well cared for and things you won't see in a Petsmart. Although, I've got those around here too and I generally buy supplies there because they're cheaper. I've always wanted to try ordering fish online as someone previously suggested.
I get my food and supplies from Kens, and most of my fish here or elsewhere on line. I have a petsmart/petco, each about a mile from my house, and I will once in a while get fish there (neons and glass cats). I also visit Uncle Neds, about an hour away, when they have something I am looking for.