There's a lot of good advice here, but a few things I disagree with. Really, you should have absolutely no doubts about the breeder if you do your research.
I can't agree with the idea of buying from larger scale operations, simply because their practices are so abhorrent. Multiple stud dogs and brood bitches farmed out to "guardian" families, bitches being overbred and on consecutive seasons, puppies being neutered before sale, which is detrimental to bone health. All of these are red flags.
Pet breeders are a very mixed bag. It can be anything from an accidental mating of brother/sister or father/daughter, to a well planned litter with all health testing in place and a proven stud dog. Most will fall somewhere in between but are best left unless you are 100% sure it's legit.
For a purebred puppy I would always advise going to shows and speaking to people in your chosen breed. Contact the breed club for their breeder list and ask for personal recommendations. Try to go with established small scale show kennels that have a good reputation, even if it means going on a waiting list for a puppy. If they want to do a home check or ask you for references, that's a good sign.
If you want a rescue, try a specific breed rescue first rather than going to one of the large charities. Breed rescues are far better placed to understand the specific problem areas in a breed and are more likely to be honest about whether a particular dog will suit you. This is particularly important with the larger, stronger breeds that may have guarding tendencies - the generic charities are not always clued up enough on the territorial instincts that may only kick in several months after rehoming.
If you have any doubts whatsoever about a breeder or a litter, walk away. Don't think you are being kind to the puppy - this is how puppy farmers continue to churn out dogs for profit. They prey on people's nurturing instincts and sensitivities.