Humane treatment of farm animals is addressed by quite a few certifications, including organic, American Grassfed Association's grass-fed standards, Food Alliance, and others.
However, as of this writing, three certification programs specifically focus on farm animal welfare:
Certified Humane Raised and Handled The livestock producer applies for and receives the certification. But CHRH will also inspect the slaughter plant to assure it meets the North American Meat Institute guidelines, and both the slaughter and processing plant for traceability -- i.e. to assure certified animals and meat stay separate from uncertified animals and meat. and inspects traceability.
American Humane This certification works similarly, assuring a plant meets AMI guidelines and that product is segregated and traceable.
Animal Welfare Approved AWA is also similar. As described in their standards:
"Slaughterhouses receiving animals in the Animal Welfare Approved program, or the process of slaughtering on-farm, must be reviewed by the Animal Welfare Approved program and pass an audit for pre-slaughter handling, stunning, and killing in compliance with American Meat Institute guidelines, with the further Animal Welfare Approved prohibition on the use of electric prods."