Greg Egan is one of the most philosophically astute science fiction writers since Stanislaw Lem. His work explores not only the classic science fiction themes, but also ethics, identity, religion, and politics. Here are a couple of terrific selections available on the internet.
On the far world Oceanic, where the special creation of humans by God is a scientific fact, ten year old Martin has a profoundly affecting religious experience. As he matures, studies and pursues his scientific career, the dogmas of his religion slip away one by one, until he is left only with the ineluctable experience itself. And then he discovers the shocking truth about both his religious experience and the origins of humanity on his world.
The Moral Virologist
Although the moral is heavy-handed and the ending somewhat weak, Egan's tale of a fundamentalist Christian's effort to enforce the will of God is especially relevant in the light of the recent demise of Jerry Falwell and the debate over the human HPV vaccine.
(Also have a look at Greg Egan's home page)