And to many other series. The dancing banana has made several cameos, and the characters sometimes mimic other characters when they fight, such as Mario imitating Neo and Sonic doing the Tatsumakisenpuukyaku in Episode 5 or Mecha Sonic performing Akuma's devastating Shun Goku Satsu attack in Episode 6.
In an attempt to get out of exploring a potentially-scary area, Luigi tries to leave, putting a cardboard cut-out of himself in his place. Said cut-out is Weegee (aka the memetic mutated version of him seen in Mario is Missing!).
The sound effect Kolorado's stopwatch makes is Lavos' roar.
In Episode 8, a shout out is made to Hotel Mario, when the characters find a letter which Bowser wrote almost word-for-word as in that same game (including a crossed out portion about hotels), with an instruction book containing a lampshading and the terms for Peach's release included!
Episode 8 also features a shout out to Star Trek with the minion who "jus' cayn't" push the stuck button to the Omega Doomship's BFG.
There's a shout out to both Peanut Butter Jelly Time and Foster's Home for Imaginary Friends when Wario and Waluigi are exploring the Pipe Maze in Episode 7. They go down a pipe that Mario and friends just went down into. They try to go down the pipe when the PBJT Banana comes out, yelling out "I LIKE CEREAL!!!" It results in a massive explosion that makes Wario and Waluigi crash into the two main characters from Bowser's Kingdom (a now-canceled flash series made by one of Alvin-Earthworm's friends), Hal and Jeff.
The song played on Episode 8 during the argument comes from Skies of Arcadia. It's the song played when you enter Valua City.