Almost no games saw as much anti-Christian censorship as the Final Fantasy series. In the original games America turned churches used for resurrecting the dead into clinics. Crosses used to mark the path to Bahamut and the Crystal Rooms sported Stars of David. In Final Fantasy IV (II here) Rosa lost one of her best abilities just because it was called Pray. the Tower of Prayers became the Tower of Wishes and the Holy spell was dubbed the hella confusing White. At least Banon got to keep the Pray ability in Final Fantasy VI (III here), though it was changed to Health. By the time Final Fantasy VII was released on Playstation overtly Christian and Jewish references were no longer censored, and much of the cut material was re-instated on later re-releases of the Nintendo era games.
Here's something you probably didn't know; The Legend of Zelda is the world best Christian game series. No really. In the first game the Book of Magic started out as a Bible and Link carries a Christian cross on his shield. Crosses remained prominent in Adventure of Link, even becoming a usable item to see ghosts. By the time Link to the Past rolled around though there was an honest to God religious schism in the game. The artwork above is official, showing Link praying to Jesus before embarking on his quest. Despite that other Christian aspects like the word pray and Link genuflecting were cut. Nonetheless that game introduced the now-canon Goddesses in-game religion, leaving Christianity behind in further releases. Still, there's no doubt about it; The Legend of Zelda began it's life as the tale of a righteous Christian warrior who had his faith largely erased in the name of marketing.
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