The way RPGs handle religion is something of a meme. Are bad things happening? Might want to see what the local bishop is getting up to. An evil organization is oppressing the masses? It's probably the church. You should go kill god while you're saving the world, just to be on the safe side. Bandai Namco's Tales series, Breath of Fire, sometimes Falcom's Trails series — these and a whole lot more use religion as an easy caricature for villainy, liberally borrowing iconography and concepts from real-world doctrine to lend a sense of legitimacy to their stories.