Father Maxi making his way through the underground is taken from the Atari game Pitfall
The great Queen Spider was taken from the 1974 Doctor Who episode Planet of the Spiders: Part One (1974).
The plot for "Red Hot Catholic Love" was inspired by real world events. Early in 2002 the news reported a massive conspiracy in Boston to cover up priests raping children for decades. Later there were reports all around the world of similar events.
An earlier episode of South Park was called How to Eat With Your Butt. In this episode, people figure out how to do that very thing.