My nephew got a hamster from PetCo and it was the sweetest thing. I have a hamster now who came from a small, locally owned pet store where I've bought many guinea pigs, hamsters, and gerbils and they took excellent care of their pets. The same lady owned the store for many years and was always there and she was always spending time and talking with the animals. Every single pet that came from that store was happy and healthy. Sadly, due to the economy, that pet store has closed so the last time I got a hamster I had to buy from the nearest pet store in our local shopping mall. There's a difference in our pets, as the mall hamster is not as tame, she was kept in a cage in a corner of an enclosed room, with no wheel or toys in her cage. Her neighbors were mice, hamsters, and snakes. Yes, snakes. The first time I saw her was last December and she was still there a month later, so I just had to have her. It's been almost a year now and she's still not nearly as tame as the hamster that we bought from the small mom and pop type store. But I love her and wouldn't give her up for the world.
Anyways, my point here is that it's not the pet store itself, but the STAFF that makes a difference in your pet. If the animal has been hand trained and well cared for right from the start, whether it's by the breeder or the pet store, then you have a good chance of bringing home a good pet. The best thing to do is to browse each store's selection during the evening, when the animals are active. When choosing a pet, make sure you handle several different animals. A hamster may be shy or nervous since it doesn't know you, but signs to watch for would be if the hamster flips on its back, chattering its teeth and shielding its face with its paws. Those are signs that a hamster will not be as friendly and will be harder to tame, if ever. That's how our little female hamster behaved, and although she's not as anti-social as she used to be, she's still not nearly as sweet as our other hamster.
Another point: a friend of mine worked for both PetSmart and PetCo and confided in me that both companies got their stock from the same exact breeders.... so it doesn't make a difference which company you choose to go through.
Good luck on finding your pet...