Short story: the Marquis de Sade's "Dialogue Between a Priest and a Dying Man"

This is actually a dialogue rather than a story. A priest is giving the last rites to a dying man who repents that he has not taken full advantage of the fact that he was "created by Nature with the keenest appetites and the strongest of passions and was put on this earth with the sole purpose of placating both by surrendering to them." The dying man then proceeds to state his case for atheism.

Despite the fact that the dying man seems not to have heard of the is-ought fallacy, he makes some good arguments that resonate well with current debates. His opponent is probably an unfair strawman, but I have heard a Christian apologist in a recent debate with Christopher Hitchens advance at least one of the priest's counter-arguments--the notion that the world has been created "broken" as an answer to the problem of evil.

The dialogue is far too long to reproduce here, so I'll just provide a link to the PDF:

"Dialogue Between a Priest and a Dying Man"

Of course, more than just atheists have been influenced by de Sade's ideas: