Just a few charitable atheist organizations.
The main atheists charities being Médecins Sans Frontières, Médecins du Monde and Aide médicale internationale Which I think you will find are in every other war-torn or famine ravaged country in the world.
Center for Victims of Torture
Human Rights First (formerly Lawyers Committee for Human Rights)
Human Rights Watch
Gifts in Kind International
Action Against Hunger – USA
Food Bank for New York City (formerly Food for Survival)
Reading is Fundamental
Population Action International
Big Brothers/Big Sisters of America – N.O.
Homes For Our Troops
Compassion & Choices
National Alliance for Research on Schizophrenia and Depression (NARSAD)
Mental Health America (formerly National Mental Health Association)
American Foundation for Suicide Prevention
I R Teams
Direct Relief http://www.squidoo.com/Atheist-Charitieshttp://www.charitywatch.org//toprated.html#envirohttp://coreysviews.wordpress.com/2010/12/22/list-of-atheist-charities/