Best Friends, in Utah, is a no-kill sanctuary for all types of animals.
http://www.bestfriends.org/
Alley Cats, headquartered in Virginia, focuses on TNR for feral cats.
http://www.alleycat.org
No Kill Advocacy Center, in Oakland, educates organizations and individuals in creating a no-kill society.
http://www.nokilladvocacycenter.org/whatsnew.html
Morris Animal Foundation in Denver, uses 100% of donations for animal research.
http://www.morrisanimalfoundation.org/
Humane Society, United States, in Washington DC, promotes humane treatment of all animals.
http://www.hsus.org/
North Shore Animal League, in New York, is regionally based, but also has programs nationally.
http://www.nsalamerica.org/