His arcade ending in the DC crossover has him being weakened under Earth's sun, but being able to regain his power so long as he keeps a mysterious green rock nearby; this is an inversion of how Superman's powers work.
Likewise, his Torpedo special is renamed as "The Superman".
In the official Mortal Kombat comic book, Scorpion grabs Sub-Zero and tells him to look into his eyes. This is an even clearer reference to Ghost Rider and his Penance Stare power.
After defeating Scorpion in Shaolin Monks, Scorpion gets dragged into the lava by skeletons. As his arm goes in, he gives the player a thumbs up. This is a reference to the ending of Terminator 2: Judgment Day, in which the T-800 (Arnold Schwarzenegger) gives John a thumbs up before he gets engulfed by molten metal.
Jax's fatality in Mortal Kombat 3 in which his arms turn into blades is likely a reference to the T-1000.
In MK vs DC, his ending is very similar to Cyborg's origin story.
In 9, one of his fatalities is a shot-for-shot copy of Tak's Fatality in War Gods, another Midway project. If you remove the kick at the end, it's also a shout-out to one of Superman's Heroic Brutalities in M Kv DC.
In X, if his Carl Weathers-inspired costume is chosen and his opponent is Johnny Cage, they recreate the handshake from the original Predator, complete with "You son of a bitch!"
In 4, her facial features are modeled after Talisa Soto, the actress who portrayed Kitana in the theatrical adaptations.
In 9, her chapter during story mode contains a scene very much like one found in Alien: Resurrection where she finds a lab filled with progressively more human half-breed clones of herself.
Her Arcade Ladder ending has three Edenian women re-united to fight for justice all over the realms; as the narrator explains this, the three characters are posed in silhouette over an orange background and as the ending fades to black, the music closes with the iconic jingle from the show.
Kung Lao's weaponized hat gimmick was inspired by Bond's villain Oddjob.
Cyrax and Sektor seem to be ripped right out of Predator. If you ever had doubts about this one, Cyber Sub-Zero from 9 and Predator himself in X makes it even more obvious.
Cyrax's self-destruct fatality has him typing some kind of sequence in a panel in his pulse, like the Predator himself. Later games show that Sektor and Cyber Sub-Zero have similar panels.
Cyrax uses a "Sabre of Light" in 4. In the PS2 games, Sektor also uses that and was renamed as "Pulse Blades": A blue one (green in Armageddon) for Cyrax, and two red ones for Sektor.
If Ermac gets knocked off Raiden's Sky Temple in Deception/Unchained and Armageddon, and sent plummeting to his death, he's got two words for ya: "SUCK IT!!!"note Although many fans incorrectly believe he's dropping an "F" bomb instead.
Speaking of Star Wars, Kabal was burnt alive, horrifically scarred, and forced to wear a respirator & hide behind a mask the rest of his life, a possible reference to Darth Vader.
One of the game over messages in Shaolin Monks is "Kabal says thank you very much." Aside from referencing the mission in which you can rescue him, Kabal's voice acting appears to be modeled after Elvis Presley.
Rain's costume is purple, there's also his name, and Armageddon reveals that he's a Prince. Explanation Prince has a song called "Purple Rain".
Sheeva's namesake is Shiva, the (male) Hindu destroyer god with multiple limbs. Like Shiva, Sheeva has extra arms and is turned into a destroyer goddess in her Armageddon ending.
Her arcade ending in 9 involves the Shokan taking control of Australia with the permission of world leaders. This is a possibly reference to Lex Luthor in Superman II. This may also be a reference to the fact that 9 is Banned In Australia.
Stryker's design in 3 has him resemble Woody Harrelson to a good degree.
The original Quan Chi is somehow similar to Spawn's demon-in-the-guise-of-an-evil-clown, Violator.
Reiko's original design in Mortal Kombat 4 bears more than a passing resemblance to Nightwing.
In the X comics, he suffers a superpower meltdown due to not being the chosen one of an ancient legend. Now, replace the ancient legend with the Orochi legend and you have the MK version of Rugal Bernstein.
"Cyborg" face: It resembles that of the T-800 from the Terminator franchise.
"Skull Tattoo" face : A face tattoo that resembles the face paint skull warn by Image Comics character Chapel from Youngblood and Spawn.
"Eye Stripe" face: Based on face paint worn by Pris Stratton in Blade Runner.
"Anime 1" hair (female): Based on that of Ryoko Habuki, though the default color is light green rather than aqua.
"Anime 2" hair (female): Based on that of Sailor Moon's odango-and-twintails (though the default color is blue instead of blonde). In addition under Head Accessories is "Tiara" which strongly resembles those worn by the Sailor Senshi.
"Anime 1" hair (Male): Based on Cloud Strife's (though default color is light blue instead of blonde).
"Anime 2" hair (Male): Based on Goku's. In addition, there is also under Torso "Layered Gi" which is based on his and Krillin's most common outfit though without any Kanji on the leftside chest or back.
"Devil" and "Wave" hairstyles: Based on respective Street Fighter characters Akuma and Guile.
"Swoop" hair: Based on Kazuya Mishima.note There is also a hairstyle called "Pillar" that is default blonde that has some resemblance to that of Paul Phoenix's, but Phoenix is neither the only nor first character in fiction to sport a Hitop fade hairstyle and thus debatable on that one.
"Crew Neck" torso and "Striped Runnig" pants: Based on the outfit warn by Bruce Lee's character in Game of Death. Clothing for female characters includes a similarly designed "Track" torso and pants which is modeled on The Bride's whose outfit in turn is based also on the aforementioned Game of Death one.
"Harness" torso: Based on that worn by He-Man (including lacking any other shirt or clothing aside from the harness) though without any sort of heraldry on it.
"Suspenders" Torso and Pants: Based on outfit of Vampirella. In addition "Wrap" (also under torso) is also very similar (minus any sort of collar).
"Daisy" Torso and Pants: A rather obvious reference to Daisy Duke.
"3 Knives" glove: Based on the claw worn by Mr. Han, the main villain of Enter the Dragon.
"Utility" belt: Based on Batman's (minus any sort of Bat symbol).
"Shield" chest accessory: The shield is placed on the back and also has a design that looks like a turtle's shell. In addition "Trident" under helmets is a holdover of the helmet of Sub-Zero in Deception, but it was in turn based on that of the Turtles' archnemesis The Shredder.
The stage Fatality for the City stage (having the opponent run over by a car) bears a striking similarity to the ending of Final Destination 4, complete with an X-ray view despite not being an X-ray attack, and leaves a twitching beheaded corpse similar to the first death in that movie.
Also, the Subway stage fatality might be a reference to The Matrix, where Agent Smith attempts to kill Neo by throwing him onto the path of an incoming train.
The new Test Your Strike mini-game has a concept similar to the test given to Frank Dux in Bloodsport, where he had to break one brick out of a pile.
Freddy Krueger has several Fatalities that are reminiscent of the most infamous kills of his home franchise:
In one, after stabbing his opponent with both sets of claws, he drags him down into a hole that has just appeared. This is then followed by a geyser of blood, similar to how he killed Glen, Nancy's boyfriend, in the very first movie.
Another has Freddy throwing his opponent into a boiler to be burned alive. This references both his own origin (Freddy was burned alive by vigilante parents who wanted to make him pay for murdering their children) and how he killed the former Final Girl from the third movie as his second kill in the fourth movie.
D'Vorah has several cues towards Sarah Kerrigan. She commands an army of insects (mutated insects in Kerrigan's case), many of her attacks involve some kind of Body Horror, two of her variations are called Brood Mother and Swarm Queen, the Comics show how she was killed, with the implication of being resurrected by an evil force, mirroring the ending of the next-to-last mission of the Terran campaign in the original Starcraft, the Story Mode has her starting in the "good" side and then showing her true colors (mirroring Kerrigan's actions in Brood War) and her ending has her declaring herself Queen of an insectoid species who conquers every other realm and slaying a powerful being, similar to the ending of Brood War.
When he uses his X-Ray on the Predator, the bullet he fires has Ugly Mofo written on it.
In the comic, he mentions that the rescue operation feels more like a Suicide Squad.
The duo of Ferra/Torr have a veryMaster Blaster-like dynamic going on, something that has not gone unnoticed by fans or commentators at E3 2014. Their playstyle in general note barring their Lackey variation, where Torr mainly fights on his own also calls to mind Chang and Choi in Capcom vs. SNK 2: Torr does the brunt of the brawling and Ferra issues orders, though several specials (especially in the Vicious variation) have her jump into the fray (and off of his shoulders) to help out.
Johnny Cage goes so far as to call them Master Blaster in pre-match intro dialogue.
Jason's Unstoppable variation allows him to resurrect via a lightning strike, which was how he was revived in Friday the 13th Part VI: Jason Lives. Said variation also gives him a chain on his neck that stuck with his appearances from that film onward.
One of Tremor's brutalities involve him turning the opponent to gold (While also impaling them in the chest with a spiked gold ball,) is called "It's Me." This is a reference to both the phrase "It's me" and Golden Freddy from the Five Nights at Freddy's series, as the two are commonly linked together by fans.
Speaking of Triborg, it is a robot with a rouge A.I. seeking the end of organic life that it deems as inferior to itself and also inhabits multiple bodies simultaneously. Sounds eerily similar to Ultron in yet another tribute to Marvel Comics.