This article is continued proof that there is a great deal of misinformation circulating. It actually depends on what you are looking for. Your local vet can be a great help in helping you to find a good, healthy dog.
If I am looking for a particular breed...I would definitely go for a reputable breeder. If the breed is not so important...then the shelter or the family down the street with “accidental” pups can be good options.
Either way, the only “pets” you should ever consider buying from a store would be things like gheckos or hamsters. Dogs and cats should only be bought from reputable breeders (verify from a good vet that the breeder is a reputable breeder and not just a back yard breeder akin to puppy mills) or adopted from shelters or rescue organizations.
When you buy a dog or cat from a pet store, you are buying an animal that was bred in a puppy mill or its feline equivalent. The breed registration papers for that animal might be valid, but they do not ensure that you are getting a healthy or quality stock animal.