What can be wrong with a dog if she seems very lethargic laying down all day but has a good appetite and good bowel movements?

Could she possibly be pregnant? There could be many causes-take her to the vet. Dogs can get illnesses and conditions like humans, such as tumors, leukemia, viruses, etc.

You don't say how old the dog is. As dogs age, they tend to be less active. There may also be an issue such as heartworm that is causing the dog difficulty with physical exertion. Have a vet do blood workup and parasite tests. Dogs mask illness and injury well so if she's showing outward signs such as lethargy it may be a serious problem.

I agree with both of the above statements: I believe that it is really in your dog's best interest that you consult your vet about your concerns and let him/her decide what the best course of action "if any at all" should be taken to remedy the situation. Kechara

Possible signs of diabetes or cushings disease

http://k9diabetes.com/forum/index.php?referrerid=18