Patricia McConnel has a section in "The Other End of the Leash" about well-built dogs, and what makes them healthier. Basically it ends up being a dog that is built pretty much like a wolf, but smaller - 40-60 pounds I think. The dog would have prick ears (floppy ears tend to hold in moisture and have more infections), long nose (short-nosed breeds like pugs tend to have breathing difficulties and cannot handle hot weather), a back that's length is proportional to the length of the legs, a chest that's not too deep, long and thick tail, relatively narrow shoulders (not wide shoulders like bulldogs), etc.
Besides that, I do agree that the less popular a breed is the healthier it is.