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.
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.
"Ello Guv'nor" was inspired by the endless number of low budget slasher films where the killer is a possessed object.
"High Score" features Mordecai and Rigby trying to get a high score on an arcade game, only to be thwarted by a giant bearded face. Isn't there a famousDonkey Kong player with a bearded face?
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 Pro 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 "Viral Video", you can see Antoine Dodson of Bed 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 gotta have appropriate lyrics. Like "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.
During the chase scene near the end of Night Owl, the museum security guard on the far left looks a lot like one of the Twins from Superjail
During the movie theater scene in "Do Me a Solid", the first scene of the movie we see is a Peewee Herman look alike that says "You have a Telephone call at the front desk".
The same episode features a Shake Weight commercial.
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.
"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.
Possibly a coincidence, but the opposing team is the Magical Elements, and the camera pans past a sign for "Sweet Petites: Cupcakes to die for!" Incidentally, shortly thereafter, MLP itself did a bowling episode.
The Halloween Special has at least two references to J.G. Quintel's old NSFW student film 2 in the AM PM: 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.
"Eggsellent" has Mordecai pick the 'eggsellent' net hat out of a bunch of different hats all reading 'eggsellent' on them similar to the climactic 'choosing of the grail' scene from Indiana Jones and the Last Crusade.
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).