Purchasing from a pet store is like any other major purchase...you need to do your homework. Doing this, however, meant that we had to put our spur of the moment emotions aside every time we saw a dog we just "had to have."
We purchased our puppy from a store, but only after doing considerable research, asking the store for references of others who have purchased from there, and asking around to other pet owners for their feedback.
We also took visits to the store to see their puppies. The dogs at the store where we purchased from were always alert and awake. They were playfull and, well, puppylike. The puppies also played in pens together, rather then being individually crated. The pens were very clean, as were the dogs. The puppies were well documented, with information from the breeder should we wish to contact them to find more info about the parents of the dogs.
I've visited other stores and didn't get the same feeling. In fact, going to some of the local malls, it seemed as though some of their dogs were drugged...the dogs were very sluggish and did not act like you'd expect a dog to act when seeing new faces. The mall dogs were dirty, the place smelled, and some dogs were in crates way too small.
This is the problem with pet stores, there are too many who don't care about their animals, and are just looking for the profit. The one diamond in the rough that does show they care about the animals get lumped in together and get a bad rep. That is why we made sure to do our research. The last thing we wanted was a dog with health problems and social issues from not being treated properly and not being with other dogs.