Phoenix - No doubt, there are a lot of irresponsible 'puppy mills'. Just as you are now looking for a Dobie with good qualities, we really did our homework. My wife first saw the father or Rommel in her work as a Vet Tech, and we spent a lot of time researching breeders as we did Rottweilers. By researching the breeder and even checking with others who have dealt with them, you can usually get a good idea of how much they care about their animals.
The breeder in which we purchased Rommel had about 20 years experience in breeding/handling/showing ONLY Rotts. Hell, the paperwork packet we received was an armful regarding past history - family tree goes back about 5 generations and such.
One important thing to remember is that go with a breeder that cares about what happens to the dog once it leaves his/her ownership. We actually had to sign a contract regarding the care of the dog, plus there is a clause which states, if we no longer wanted him, we would return ownership to the breeder.
Puppy mills just plain suck, and it really is a pain to see such dogs locked up in a petshop. Theres a slew of Dobie Rescue firms as well, just as for pretty much any other breed. With all the dogs in kennels and shelters, it still amazes me why people shop from run of the mill mall petstores for a dog.