Contracts
Most reputable breeders will only sell a pet under a written contract. It should state the breeder's policy regarding health warranty and refund/return. It should also explain any other responsibilities of those involved.

Support
A reputable breeder will offer you lifetime support with your pet.

Knowledge
A reputable breeder will be knowledgeable about the breed and the genetic diseases common to the breed.

Cleanliness
The breeder's kennel or home should appear clean and orderly.  They will probably ask you to wash before handling puppies, maybe even ask for you to remove your shoes.  Disease can be carried in on clothing, tire tracks, etc.  Many breeders will not allow visitors when young puppies are in their home or will not allow visitors in the kennel area. They will only allow visitors once puppies have been vaccinated.  

Frankness
A reputable breeder should be willing to answer all your questions about the breed and tell you how to care for your pet. The animals should appear clean, healthy, and happy. 

Screening
A reputable breeder will ask you questions about your life and home to make sure that the animal they place with you is a good fit for you and your family.

Records
The breeder should have extensive breeding records, pedigrees for the sire and dam, and health records, and be willing to share this information with you.  A breeder who is unwilling to reveal this information should be cause for concern.

Do you provide a written contract? What health warranty do you offer?

What health examinations have been performed on the parents of the animal?

What vaccinations and treatments have been given to the animal?

Are the animals being raised in a home or kennel? If raised in the kennel do they have comfortable conditions, heat and ac, not over crowed....etc

How old is the animal?

Is the animal neutered/spayed? Do you require a spay/neuter contract?