Final Fantasy games are pretty blatant in their anti-religion stance, off the top of my head there's a guy in Camp Drybone that questions the whole Ifrit thing - "worship me or burn in hell for eternity, doesn't sound like much of a choice to me" which is clearly a dig at Christianity. There's probably way more that more observant players will have picked up on than that one snippet that caught my attention.

This vid does a good job of putting together the pieces from previous titles- http://youtu.be/MLhiWw3pzQk