Given a Call Back in Super Paper Mario. His hint about the (Japanese) art style of Chapter 6 is "I like the art direction of this place because the art direction is really nice, and whoever the art director was did a really nice job in the art direction, yea, it's Japanese."
Similarly, he absolutely loves the soundtrack of MOTHER 3.
He even lampshades it in part 10: "Huge feet is a RUNNING GAG"
Also in Pokémon Colosseum, there's a counter for the number of times the Dumb AI uses an ineffective normal, ground, or fighting move on the ghost type with Levitate Misdreavus. It finished the game at 31, plus a Confuse Ray when it was already confused.
Another rather unfortunate running gag in Pokémon Colosseum is him failing to catch the bosses' Shadow Pokemon.