* For starters, it's a WholePlotReference to ''Anime/DragonBallZ''.
** Mario's super fire blast attack (as well as the blast Mecha Sonic uses to [[spoiler:finish off Axem Red]]) is a direct homage to Goku's infamous [[KamehameHadoken Kamehameha]].
** The huge evil energy sphere that Mecha Sonic uses to [[spoiler:destroy Yoshi's Island]] is an awful lot like Frieza's infamous planet-killing Death Ball.
** The Game Boy-style Emerald Radar, which much like the Dragon Radar from Dragon Ball was designed by a GadgeteerGenius and even used an Emerald to study for its effects.
** While we're on the topic, the situation on Mobius ([[spoiler:most main heroes dead, the end of the world being imminent]]) smacks of the Trunks's future in DBZ.
*** Especially with Dr. Eggman and the creation of Mecha Sonic in general, a direct homage to the creation of the Androids from Mirai Trunks's storyline.
** And then there's [[SuperMode Super Sonic]].
* 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 [[Film/TheMatrix Neo]] and Sonic doing the [[StreetFighter Tatsumakisenpuukyaku]] in Episode 5 or Mecha Sonic performing Akuma's devastating Shun Goku Satsu attack in Episode 6.
* Not to forget ''{{WesternAnimation/Futurama}}'':
-->'''Sonic:''' Bite my.... spiney... blue... butt.
* 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 [[Memes/VideoGames memetic mutated]] version of him seen in ''MarioIsMissing'').
* Some of Mecha Sonic's abilities appear to be based on [[{{Metroid}} Samus Aran]], and [[{{Leitmotif}} the music played before he appears]] was originally used for the same purpose for Dark Samus.
* The [[SpoilerOpening spoileriffic anime-style opening]] uses the second opening theme for ''MegamanNTWarrior''. This is a ShoutOut to ''TVTomeAdventures'', which also used that song for its opening.
* Ludwig von Koopa calls Bowser "King Dad", a reference to the ''Super Mario Bros.'' cartoons.
* A musical ShoutOut to ''Franchise/TheLegendOfZelda'' is used when Mario gets the silver Emerald, immediately {{lampshaded}} by Professor Kolorado:
-->'''Kolorado:''' Uh, Mario... I think that's [[BreakingTheFourthWall the wrong video game series]], old bean... [''Cue FaceFault'']
* The sound effect Kolorado's stopwatch makes is [[VideoGame/ChronoTrigger Lavos' roar]].
* In Episode 8, a shout out is made to ''VideoGame/HotelMario'', 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 [[LampshadeHanging a lampshading]] and the terms for Peach's release included!
* Episode 8 also features a shout out to ''Franchise/StarTrek'' with the minion who "jus' cayn't" push the stuck button to the Omega Doomship's BFG.
* Basilisx owes a lot to {{Wolverine}}'s moveset from the ''CapcomVsWhatever'' series.
** As does Axem Red's aformentioned {{BFG}}, which was lovingly ripped from IronMan's moveset.
* Another one from Episode 8 comes from Basilisx's final attack on Mario after the Poison Mushroom attack. It looks exactly like Vega's Ultra Special from ''VideoGame/StreetFighterIV'', "Bloody High Claw".
** Not to mention Sonic doing the Tatsumaki Senpuukyaku, from the same series, several times. Also, Mario doing the Shoryuu Reppa in Episode 8. Mecha Sonic also uses Akuma's Shun Goku Satsu at one point.
* [[spoiler:Robotnik]] [[Anime/NeonGenesisEvangelion holding his hands in front of his face, with his glasses shining.]]
* There's a shout out to both [[http://www.youtube.com/watch?v=s8MDNFaGfT4 Peanut Butter Jelly Time]] and ''FostersHomeForImaginaryFriends'' 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 ''BowsersKingdom'' (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 ''VideoGame/SkiesOfArcadia''. It's the song played when you enter Valua City.
* When [[spoiler:Toadsworth collapses because of Peach's kidnapping]], a ScareChord plays. [[MortalKombat Guess which one.]]
* [[ZeroWing "Main Screen turn on." "We get signal."]]
* A Mook with a thick Scottish accent says he can't fire the main cannon, [[Series/StarTrekTheOriginalSeries as he doesn't have enough power]].
* And, for that matter, the Koopa Bros being "King B's [[Franchise/TeenageMutantNinjaTurtles ninja heroes in a half shell]]"
* Wario using Waluigi to get to Yoshi's Island (as a life preserver) might be a ShoutOut to ''MarioAndLuigiSuperstarSaga'', where Luigi is used as a surfboard, more or less.
* One Koopa Bro spouts the "Smell ya later!" line, after their first encounter with the main team, a la [[VideoGame/PokemonRedandBlue Gary Oak/Blue/Green/whatever]].
* Semi-Super Mecha Sonic's response to Red's "YouMonster" remark is a direct paraphrase to Broly's infamous "I am the Devil" line.
* During Mecha-Sonic's NoHoldsBarredBeatdown of the Axem Rangers, he quotes [[VideoGame/FinalFantasyI Garland]]. [[{{Dissidia}} "I'll crush you!"]]
* Basilisx's underhanded tactics, especially using loved ones as a shield, mirror those of Eis Shenron in ''Anime/DragonBallGT''.