Breeding dogs, horses and humans

I've been looking over our community outreach program lately, and it reminded me of how much dog (and other domesticated animal) breeding bothers me.

If you're a dog lover, then you're aware of the various *inherited* health problems for the different breeds (and if you're not a dog lover, then you've just learned something new!).  These health concerns are the result of genetic engineering through breeding.  Breeders will find 2+ favorable characteristics in 2+ breeds of dogs (or other animals).  After X# of generations, a new breed of dog emerges with said favorable characteristics, but also at least a few serious health problems.

There are benefits to this practice, to be sure, but I can't help but question it when comparing the benefits to the genetic harm it's causing to the dogs.  Also, I know full well that eugenics programs (breeding programs for humans) have long been recognized as immoral and inhumane.

Sure, the domestication of animals has been an integral part of humanity's development, from hunting partners (wolves/dogs) to helping streamline the work on the farm (horses/oxes) to transporting people and things (horses, camels, etc.); but I think we're at a point where - by and large - we can probably cut back on this.

One of these days I'm going to have to sit down with an animal breeder and a geneticist and a philosopher and we'll sort this whole thing out.  Until then, I'm very interested in what other people think.