I want to preface this by saying that I COMPLETELY agree that pet stores shouldn't be allowed to sell dogs and cats. However, I do have one dog that was purchased at a pet store. It's a little mom and pop shop where I used to live, and they take great care of the animals. I don't think that their animals come from puppy mills. Kittens have large, tall cages with toys, scratching posts, and platforms. They are handled regularly and they live with their littermates. Puppies are walked multiple times per day and the cages are all pretty clean. Small puppies are kept in cages in the front window, large puppies are kept in pens on the floor. The store's owner is a vet tech and they really seem to care for the animals.
I was looking in the store soon after my beloved Akita (a shelter dog) had died. I found a 6 month old pom/eskie mix that a family had brought in- for one reason or another they could no longer keep him. Since he was older than the other dogs, he had been there for a while. I fell in love and bought him- he was so much sweeter than the pure bred dogs I had been looking at before I saw him. Yes, I feel guilty about buying a pet store dog, but he has the most wonderful personality, and is in perfect health other than occasional bouts of colitis, which I'm told is common in small dogs. He exhibits none of the unsocialized behaviors or congenital defects that are so common in puppy mill puppies. Sometimes you just know that a dog will be the perfect match for you.
Also, I just wanted to reiterate that, for the folks like me that can't bear to go in an animal shelter, remember adoption programs and rescues if you're considering a dog! Every pet that gets adopted from these programs frees up another spot for a dog in a shelter. I got my second dog from the Petsmart adoption center, and my third from a toy breed rescue. The second dog is a shepherd mix and has done really well with us other than some food aggression issues. The third one, a pom mix, was rescued from a puppy mill, and the resulting lack of socialization was painfully obvious when we got him. It took him a couple of months to really warm up to us, and now he's very clingy. It took this dog over 4 months just to play with a toy! He's still very slow to warm up to new people, but is the sweetest dog you could ever hope to have.
My point is, even a "damaged" dog can be a perfect match, and can turn out to be a better friend to you than a pure bred dog. And if you must have a pure bred dog, check breed rescues through Petfinder before you make your final decision to buy from a breeder. Most even have pure bred puppies!!!