The Secular Web – atheist resource operated by the Internet Infidels nonprofit organization.
About Atheism – Austin Cline’s About.com page. One of the best online introductions to atheism.
Friendly Atheist – a blog and podcast providing news and interviews relevant to the non-belief community.
Freedom From Religion Foundation – an organization dedicated to preserving the separation of church and state.
Worldview Naturalism – resource on the worldview of metaphysical naturalism. Also features a collection of hundreds of atheist-theist debates.
Skeptic’s Annotated Bible / Qur’an / Book of Mormon – an extensive database of criticism of religious texts.
Early Christian Writings – the best resource for scholarship on Christian documents.
LIVIUS – a wonderful resource on ancient history, with a wealth of information on first century Judaea.
Conversations from the Pale Blue Dot – centers around philosophy, atheism, religion, ethics, and rational discourse. Unfortunately no longer producing new episodes.
The Humanist Hour – official podcast of The American Humanist Association featuring a wide variety of guests speaking on topics related to politics, philosophy, religion, science, and more.
Rationally Speaking – a presentation of New York City Skeptics hosted by Massimo Piglucci and Julia Galef, Rationally Speaking endeavors to “explore the borderlands between reason and nonsense”.
Reasonable Doubts – presents a critical and atheistic perspective towards religion with a panel of skeptics, including professors in subjects such as philosophy, psychology, mythology, and religion.
Skeptic’s Guide to the Universe – focuses on critical thinking, reason, and the promotion of science understanding.
Unbelievable? – British Christian radio/podcast show. Often features dialogues between theists and atheists.