The system Mordecai and Rigby play on some episodes looks uncannily like a Sega Master System, right down to the controllers. It's very obviously just a Master System with the name politely avoided. The episode "Over the Top" even featured Guitar Hero-like controllers with Master System controllers inserted into them and the use of the Konami Code to avoid bottles thrown by angry concert attendees.
One episode explicitly show the box art of one game, and confirms that it is a Master System (all Master System games have the same white grid background).
A Death Punchies Shout Out: When Mordecai Death Jumps out of the lava pit with Rigby, the position he flies in is obviously a shoutout to Superman.
"The Unicorns Have to Go" features a delinquent unicorn dressed like Alex from A Clockwork Orange.
In "Don", if you take notice of the many pictures hung up in Don's living room, especially the ones around the portrait of Don and Rigby, they are a fairly blatant homage to the work of pop artist Patrick Nagel.
The movie in "Grave Sights" is a huge homage to horror movies. Mordecai tries to rent an Italian film called Libraria, Zombocalpyse strongly resembles Army of Darkness complete with Bruce Campbell lookalike hero, the cover art of Zombocalypse resembles Doom, the shot of the zombies reanimating in their graves looks similar to Return of the Living Dead, and the concept of a movie creating zombies might be a reference to Demoni.
And on the video game side, the ultra-strong zombie at the end is similar to the Tank from Left 4 Dead.
The zombie chick who almost bites the main character before Rigby bumps into the projector might be a nod to the "horror hags" from the original Evil Dead.
In "Really Real Wrestling", Fourarmageddon slapping Mordecai and kicks Rigby while asking 'Is this fake?' due to them claiming it as such is a Shout Out to the infamous 20/20 interview where David Schultz slaps John Stossel twice for claiming Professional Wrestling to be fake, asking him was the slap 'fake' each time.
Fourmageddon and the snake/lizard wrestler seemed to be based off of Goro and Reptile.
Death on a motorcycle. I'm pretty sure that's a Soul Music reference.
Death also bears an uncanny resemblance to Lemmy from the band "Motorhead", right down to his accent and the two moles on his left cheek.
When he's not wearing his jacket, he's dressed strikingly similarly to Equius Zahhak, as well.
Two of the main characters of Problem Solverz can be seen in the background in 103.
During the sequence in "Grilled Cheese Deluxe" set to "Lies" by the Thompson Twins, there is one shot that closely resembles that song's music video.
"More Smarter" has Rigby dream about solving the "Hardest Math Problem in the World." This scene is taken almost directly from Rushmore and even has similar music.
Same episode: One of the answers in Rigby's crossword is "Algernon." Not the first time that name and this plot have been seen together.
In "Go Viral", you can see Antoine Dodson of invokedBed Intruder fame on a screen in the Internet Warden's prison.
And at the end, when Mordecai and Rigby are gloating over winning their bet, you can see Tourettes Guy in the crowd of people with them.
You can also see the Peanut Butter Jelly Time banana when everybody is escaping.
The "lamest, cheesiest, most repetitive song ever" includes lyrics such as "partyin'".
Skunked is one to the Incredible Hulk, with a pan to Rigby's eye when he changes and the change to a stronger berserker form triggered by rage, not to mention the regular person being horrified by his actions as his other self.
In the blonde episode, Mordecai goes to a department store called Mervington's, an obvious shout-out to the defunct Mervyn's department store chain of California.
In "Stick Hockey", Mordecai and Rigby face Chong, a character who looks virtually identical to the villain Tong Po from the 1989 Jean-Claude Van Damme movie Kickboxer, in a Stick Hockey game to the death. This sequence strongly resembles the climactic fight scene of the movie.
I'm not sure if this is a coincidence or not, but at the beginning, Benson steps in gum, just like Squidward in "Keep Bikini Bottom Beautiful". He gets way less mad about it though.
"Skips Strikes" contains several lines from The Big Lebowski including "Yeah, that's just your opinion man" and Rigby and the villains proclaiming each other to be out of their element.
The Halloween Special has at least two references to J.G. Quintel's old NSFW student film Two In The AMPM: The cop and the fart gag. Might be because 2 in the AM PM takes place on Halloween.
The episode "Bet to be Blonde" opens with Mordecai and Rigby playing a game very similar to Elevator Action.
Skips destroys a computer by swinging a sledgehammer at it, a-la Apple's 1984.
"Eggscellent" has Mordecai pick the "I'm Eggscellent" net hat out of a bunch of different hats all reading "I'm Eggscellent" on them, similar to the climactic "choosing of the grail" scene from Indiana Jones and the Last Crusade.
Later on, in "Ace Balthazar Lives", the 'knight' guarding the Eggscellent hats reappears and runs into a mosh pit, only to be knocked down instantly. His response? "I moshed... poorly"
At the very end of the episode, a new eating challenge is presented for a 96 ounce steak, probably a nod to the "Old 96er" from The Great Outdoors.
In "Video Game Wizard", there is a commercial that is an obvious reference to the Power Glove, as well as the movie The Wizard.
The kids that Mordecai and Skips compete against are even named Fred (as in Savage) and Jimmy (which was the name of the main character in The Wizard).
Also, the referee has the exact same hair style as Philip J Fry.
One of the people Rigby invited to the pizza party in "Replaced" is named Geo Dude.
Also in Replaced, the hipsters who briefly get Mordecai and Rigby's jobs are named Chad And Jeremy. This is the same as a folk duo from the 60s. The glases worn by one of them are also similar to the ones seen in this image◊. It may have been a coincidence, but hipsters are known for listening to folk music, especially that of the 60s.
In "Sugar Rush", as Mordecai, Rigby, Skips and Pops race to buy a replacement set of donuts and come back to both the park and 'regular time' before the meeting set up by Benson, near the end the music and imagery seems to reference Inception, especially on the blasting horns that start the closer the group gets back to the park.
In "One Pull Up", Muscle Man imitates the losing horns from The Price Is Right when Rigby fails to do a pull up. Later, his training with Eileen is an obvious shout-out to Rocky.
Also Rocky-related is the equipment Rigby uses to get muscles really quick. It's called The Russian and references Ivan Drago's training routine in Rocky IV.
In "That's My Television", RG-B2's name is likely a reference to R2-D2.
When Pops arrives at Skips' house to play Drawesome, he says "I got my pencil! Gimme something to write on, man!", which is from Van Halen's "Hot for Teacher".
One can't help but think that the battle sequence in "A Bunch of Full Grown Geese" is reminded of the battles within the Power Rangers series.
You could pretty much say that "A Bunch of Full Grown Geese" is full of references, for starters, the Mega Geese resembled the Doublas M2 from Mazinger Z, the Mega Ducks yelled out the name of his attack and shoots out a Rocket Punch similar to Mazinger Z and of of their attacks was the Specium Beam from Ultraman.
Another one from "A Bunch of Full Grown Geese", the Mega Ducks sorta resembled Golion/Voltron, particularly the helmet.
In the episode "Picking Up Margaret", one of the Wickets asked Mordecai to stop using his phone is the same manner of "Warriors, come out to play-aaaaaay!"; The Wickets themselves are also patterned after many of the rival gangs in The Warriors, especially the Baseball Furies.
The climactic battle at the end of "Trailer Trash" is pretty much identical to the climactic battle at the end of The Road Warrior, right down to the reveal that the convoy was a decoy and what the bad guys were looking for was somewhere else all along.
"Meteor Moves" has the Friend Zone, which is an obvious reference to the DC universe's Phantom Zone, particularly that seen in Superman II.
The World's Greatest Boss is an exact lookalike of Lumbergh.