Historical Surveys of Atheism, Freethought, Rationalism, Skepticism, and Materialism: Selected Works
There is no fixed boundary between analytical treatments of this subject matter, readers, and anthologies, on the one hand (which are now quite prevalent thanks to Hitchens and others), and historical and reference works on the other. Still, I've attempted to focus on historical surveys of varying generality and on dictionaries and encyclopedias, which are obviously basic reference works for historical inquiry.
I have preserved humanism as a separate topic, per my earlier working bibliography:
Secular Humanism—Ideology, Philosophy, Politics, History: Bibliography in Progress
As far as texts on atheism as a subject matter, my last attempt to list important recent and not-so-recent books is now quite out of date:
Ralph Dumain on atheism, irreligion, and rationality
I invite additional suggestions for this new bibliography. The most notable omission is the history of the skeptical movement—by this I do not mean skepticism as a philosophical concept, which is covered here—but skepticism in the sense of investigation of claims of the paranormal and fringe science. I know of no histories of this movement, so it is a gap that needs to be filled if the relevant literature has even been written.
I have only one possible such item of relevance (buried somewhere in my files):
Still, Arthur; Dryden, Windy. ‘The Social Psychology of "Pseudoscience"
I have not attempted to cover the history of naturalism