In the opening credits, Megas dives onto something sporting a Gundam's crest.
Speaking of that, a large amount of the design aesthetic to Evil Coop's army from "Rearview Mirror, Mirror" takes cues from the Zeon empire, from robots that look like they wear gas masks, to his own mech being a red, heavily-modified version of the original blueprint.
Captain Warlock is so obviously not based off of Captain Harlock. The name alone is one of the names Harlock's gotten stuck with in dubs.
A planet of sentient robots from "Coop d'Etat" feature lookalikes of Mazinger Z and Reideen.
Mazinger also gets a shout-out when Coop hits the "This Better Then" button - it launches a Rocket Punch with the twist that twin axe-blades sprout out of the side of the robot's fist after launch. That's Mazinger Z's trademark "Iron Cutter" attack.
In "Universal Remote", when Coop declares he'll just "hit him with something bigger," Megas folds out an arsenal that looks just like a Destroid Monster, right down the the quad shoulder cannons.
Shortly afterward, Coop turns the Megas' heater up to "DANG!", which causes the robot to link its arms together at the wrists and retract both hands to create a flamethrower — just like Combattler V used to do.
Episode 6's main villain is a Planet Eater that looks quite similar to Hellstar Remina, complete with its similar surface, appendages, and mouth. And as usual, Coop dishes out some Nightmare Retardant by blowing it up by feeding it a supercharged torpedo full of poprocks and soda.
In "Space Booty", Coop tearing open Megas's chest to grab the horn then throwing it into Warlock's ship looks like a nod to Noriko ripping out the Degeneracy reactor of GunBuster.
Ep 10 "Junk In The Trunk" features a Dream Sequence were Goat thinks about getting his own bot and his bot in the Sequence apes off the style of various Mazinger Z Franchise shows Fem Bot Mechas in appearance.
A few times, Megas puts his hands together just like Voltron to form a blazing (energy) sword.
Megas' original head unit looked almost exactly like Soundwave's.
It's seen with the Autobot Matrix of Leadership in its chest — which Coop promptly fills with processed cheese. The cheese, incidentally, comes to life.
"Ice Ice Megas" had an army of robots resembling green-colored Shockwaves, while their leader looked like Onslaught, leader of the Combaticon unit.
The villain Skalgar looks like a miniature Unicron. This is obviously intentional, as the episode never misses a chance to snark about his lacking height and plans for universal destruction.
Speaking of Unicron, how about the planet-sized monster from "TV Dinner"?
A yellow Volkswagen Beetle appears in practically every episode, sometimes TWICE in the same episode - usually getting smashed somehow.
The control unit of Mecha-Megas, despite being silver instead of black, is otherwise an obvious nod to Nemesis Prime.
You could make a drinking game out of the Godzilla shout outs in "Breakout".
The movie monster Bugra shrieks like Mothra and vaguely resembles Megalon.
The Glorft send a silver Megas clone to attack the city. It makes a roar like Mecha Godzilla. It's referred to as Mecha-Megas. Because Coop is dumb. In the end credits, Megas is walking out into the sea. Several Godzilla movies end with Godzilla doing this.
Episode 5 had the gang visit a ringworld with hostile, ancient life forms living on it. Sounds an awful lot like Halo, doesn't it?
The second episode, which features Bruce Campbell as the villain, takes place on a space station that looks suspiciously like High Charity.
Most of Megas' controls are rewired video game controllers, from a Playstation gamepad down to Atari joysticks. The "manual control" backup is Dance Dance Revolution. It also involves a pair of Power Gloves.
"Breakout" showcases expies of many video game consoles, including but not limited to: NES, Sega Genesis, Sony Playstation, and Nintendo Gamecube. Also, the title of the episode is a reference to an old arcade game of the same name.
At the end of "Bad Guy", the leader of S-Force is playing Rampage.
At the gaming convention in Vegas, Goat plays a knockoff of Dead or Alive Xtreme Beach Volleyball.
Megas even throws a Hadouken at the invincible R.E.G.I.S. mk. V.
The Transformers planet has a holy relic called the Flame of Azeroth.
And Jamie dressed as The Joker with two Harley Quinn assistants.
"BEST. THANKSGIVING. EVER."
The first season finale features four separate shout-outs to The Blues Brothers: the "Facing the Bullets" One-Liner; and a car chase through the Glorft mothership set to a blues-rock tune, complete with a dispatcher saying the line "Use of unnecessary force in capturing the Earthers has been approved."; "This place has everything..."; and finally, one Glorft mook declaring his feelings to another as death is inevitable (although hate instead of love).
T-Bot is the daringest, the uncaringest, the most belt-wearingest Mr. T parody in all of fiction! Specifically, to Clubber Lang in Rocky III.
Perhaps not coincidentally, T-Bot's name is similar to "T-Bob", the robotic babysitter from M.A.S.K.
The premise and name of the episode "Terminate Her" both reference Terminator.
Also, in "Rearview Mirror, Mirror part 1", someone is briefly seen using a hollowed out television as a fireplace like in the future flashback from The Terminator.
"Rearview Mirror, Mirror part 1" has a scene where Coop realizes he is on Earth. He falls to his knees upon noticing a lumberjack figure and yells "You maniacs! You blew it all up!". This is clearly Planet of the Apes.