A lot of the Catholic jokes clearly came from an insider, so that one is part Self-Deprecation, at least. In fact, odds are the Catholic jokes get even funnier if you went to a Catholic school as a kid.
We're looking at you, Mary Jo Pehl. Kevin Murphy also went to Catholic School and was taught by the nuns of the School Sisters of Notre Dame, so he probably had a lot to do with the nun jokes.
Critical Research Failure: Mike's speech about the honor system mentions the orator and statesman Demosthenes and his search for an honest man. The real searcher in question, however, was Diogenes, who was a philosopher legendary for trolling his contemporaries and living in a tub. He'd probably have gotten along with the MST3K crew pretty well, come to think of it.