Secularism-Freethought:
American Civil Liberties Union
Americans United for Separation of Church and State
Blue Ribbon Campaign
Freedom from Religion Foundation
Modern Freethinkers' Art from Italy
National Coalition Against Censorship
National Day of Reason
People for the American Way
Secular Coalition for America -- activist lobbying group
Secular Memorials for 9/11
 
Links by topic:

Humanism
Secularism/Freethought
Science
Religion
Atheism
General Interest