Most pet stores that sell puppies buy them from puppy mills. An ethical breeder would never sell their puppy to a pet store. Puppy mills are horrible places where dogs are bred in cramped cages. The breeder dogs spend their whole lives without ever seeing the sun, and when they can no longer have puppies, they are often just left somewhere on the roadside. The puppies are often sick and are predisposed to diseases like hip displasia or collie eye anomaly(hereditary diseases as well as many other problems too). They may appear healthy and playful, but in truth they aren't(or soon won't be). After the horrible treatment they recieve in the puppy mills(which can be compared to a factory mass producing something to sell that will cost a lot but will soon break, just after the time period for returning it is over), pet stores often do no better. One by my house keeps the dogs in tiny steel cages where they never go on walks or see the sunlight until they are bought. They are taught to potty in their cages, and more than once I've seen them playing with something dangerous- a plastic baggie that could block their airway if swallowed. I remember seeing exotic monkeys, birds, and even a tiger(as well as ducks, chickens or other domesic birds) at that store in cages near the ceiling(because the cages are stacked in rows up up up to the ceiling). Some people take pity on the puppies they find in pet stores, but that only adds to the business- if they know they will have business for their puppies, they will breed those puppies.
If a pet store by your house sells puppies(or even if it doesn't) it can become a Puppy Friendly Pet Store. If they choose to do so, they pledge to stop selling puppies(any puppies remaining in the store after 30 days must be ones purchased before signing the contract), and can showcase local pets available for adoption. Go here to print out the pledge sheet to give to the pet store.
The link above goes to a special page on this site: http://www.stoppuppymills.org/