There are frequent insulting references to MTV in the guise of "POP" music channel. Usually in the form of a sign with the "POP" channel's logo (which is very similar to MTV's) being smashed apart.
Jody Schaeffer and George Crstic used to write for MTV's Downtown, which is where they got the character Goat. This could explain the destruction of the MTV logo in each episode.
The mechs in Evil Coop's army in the episode "Rearview Mirror, Mirror" are based off of the Zaku from the Mobile Suit Gundam anime.
In the episode "Coop D'Etat", the main robots, Zanzoar and Gyven, are parodies of Optimus Prime and Megatron from The Transformers: The Movie (1986). They are also voiced by the same voice actors: Zanzoar is voiced by Peter Cullen, and Gyven is voiced by Frank Welker.
The town's school is called St. Prynoski Elementary, a reference to director Chris Prynoski.
Magnanimous's giant robot in the episode "The Return" is modeled after Ash from Evil Dead and Elvis Presley from Bubba Hotep, both of which were played by Bruce Campbell, who voiced Magnanimous.
The episode "The Fat and the Furious" is a title reference to The Fast and the Furious (2001).
The episode "Dude, Where's My Head" is a title reference to Dude, Where's My Car? (2000). This is accurate, because Coop loses his car when he allowed Jamie to use it, which is the control center (head) of Megas.
In "Bad Guy", the team who attacks Coop is the S-Force, who are loosely based on the Power Rangers. Their animalistic robots are called "Zorps", which is a reference to the Zords that the Rangers use. In addition, their master, Targon, is a reference to Zordon.
The four ladies seen in the episode "Ultra Chicks" are a reference to the leading ladies in Sailor Moon (1992).
The episode "Ice Ice Megas" is a title reference to Vanilla Ice's song, Ice Ice Baby.
"Rhat dooitronium isonier actuator thing" (as Jamie refers to it) that they put the fake cheese in at the beginning of the episode (The Fat and the Furious - Series 1) is the Autobots Matrix of Leadership from The Transformers: The Movie (1986).
The character Goat, comes directly from the short-lived animated comedy Downtown (1999). He is voiced by Scot Rienecker in both.
The T-Bot from the episode "The Return" is a combination of actor Mr. T and Gaigar from the anime series Gaogaigar.
The car that is grafted onto the Megas is a 1970 Plymouth Barracuda muscle car. The "shaker" style hood scoop indicates that is the high-performance 'Cuda model, and most likely equipped with the famous 426 cubic inch, 425 horsepower V-8 "Hemi" engine. However, listening to Coops bragging about his modifications reveals that Megas now has a 12 cylinder engine of unknown origin. The 'Cuda was apparantly equipped with a ten cylinder engine (most likely from a Viper) throughout season one, and two more are added in the episode "Ultra Chicks".
In "Buggin' the System", the creatures shown are somewhat similar to the Xenomorphs from the Alien franchise. Coop also calls their giant queen "Mothra", due to their insect-like appearance.
In "DMV: Department of Megas Violations", the bounty hunter, Darklos, is partially based on the Predator from the Predator franchise. They even have the same "dreadlocks" hairstyle.
Magnanimous bears a striking resemblance to the Marvel Comics villian, M.O.D.O.K., a character who has a unusually large head with small limbs.
The designs of the glorft were inspired by the legendary mythological being known as Cthulhu, who has a humanoid body with the face of an Octopus / Squid.
In the episode "Bad Guy", the villain Ender somewhat partially resembles Goldar (especially his wings and arsenal of weapons), who is one of the Power Ranger's greatest enemies. The S-Force could also be a play on the Rangers or Voltron.
In the episode "All I wanted was a Slushie", the drive through where Coop orders his slushies has a "W" logo, which is actually an upside down version of the "M" of McDonald's.
In "Junk in the Trunk", V'arsin's robot, the "Franken" is inspired by the transformer, Devastator, a combiner robot who is composed of construction vehicles from The Transformers: The Movie (1986).