For instance, the Civ games are basically Whig History: The Game, presenting liberal capitalism as the ideal end point for all societies. It even includes uncivilized "barbarian tribes" whose sole purpose is to be exterminated so you can take their land for the glory of capitalism.
Final Fantasy, all the way up through 10, had very strong anti-christian, anti-colonialist, and anti-imperialist themes. Gonna spoil tactics here:
spoiler
Ramza is a crusader who finds concrete proof that Jesus is not the son of god. After dealing with the political fall out of simply having this proof (assassination attempts etc), Ramza finds Jesus to be a parasite on the world literally feasting on the blood of humanity
Based.