About.com: Agnosticism/Atheism
Americans United For Separation of Church and State
Atheist Alliance International -- an organization of independent religion-free groups and individuals in the United States and around the world
Atheist Parents
buildupthatwall.com -- Christopher Hitchens, an online directory
Center for Atheism -- NYC Atheists national organization
Center for Inquiry
Council for Secular Humanism (CSH)
Free Inquiry Magazine
Ethical Atheist
Freedom From Religion Foundation
Freethought Society of Greater Philadelphia -- To promote the Constitutional principle of separation of church and state and to educate the public on matters related to a nontheist lifestance
Gay and Lesbian Atheists and Humanists (GALAH) -- Washington, DC, USA
Godless Comedy -- Pat Condell's Godless Comedy
History of Religion -- Animated map giving a brief history of the world's most well-known religions: Christianity, Islam, Hinduism, Buddhism, and Judaism
Institute for Humanist Studies
International Humanist and Ethical Union (IHEU)
Natural Atheism, David ELLER
Pharyngula -- Blog of biologist P.Z. Myers
http://philosopedia.org/index.php/Freethinkers
http://philosopedia.org/index.php/African_American_Freethinkers
Positive Atheism
RichardDawkins.net -- The Official Richard Dawkins Website
Secular Coalition for America -- Refreshingly bold freethought activism
Secular Student Alliance -- Mobilizing Students For a New Enlightenment
Society for Humanistic Judaism
The Atheist Network
The Celebrity Atheist List -- With some agnostics and other non-theists. An offbeat collection of notable individuals who have been public about their lack of belief in deities.
The Christopher Hitchens Web
The Freethinker -- The voice of atheism since 1881
The Infidel Guy
The Secular Web
The Skeptic's Annotated Bible -- "A self defense manual against biblical fundamentalism"
Theocracy Watch -- The Rise of the Religious Right in the American Republican Party