His X-Ray Move in 9 starts a butterfly kick followed by an uppercut to the chin and then a high kick to the chin. The first two moves are a homage to his Fatality in the first game, the only non-fatal Fatality in the series.
When he wins a round in 9, he makes a gesture of respect and disappears in fire. That's the same thing he does in his 3 fatality, right before the arcade console falls on his opponent's head.
Scorpion's blazing skull is an homage to Ghost Rider. This comes in full circle in the Ghost Rider movie, when Ghost Rider, while atop a skyscraper, uses a chain to grab a helicopter and pull it toward him while yelling "COME HERE!".
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 reference to Terminator 2 ending, in which the T-800 (Arnold Schwarzenegger) gives John a thumbs up before he gets engulfed by molten metal.
In his arcade ending in Mortal Kombat vs. DC Universe, Raiden finds himself being weakened under Earth's sun, but can regain his power so long as he keeps a mysterious green rock nearby; this is an inversion of how Superman's powers work.
Also in vs. DCU, his trademark Torpedo special is renamed as "The Superman".
In 2, he had a "triple" decapitation fatality that worked like the regular one, only instead of one head, Cage knocks off three. This finisher move referenced a glitch discovered in the original Mortal Kombat, where Johnny Cage could knock off multiple heads in his fatality.
In Shaolin Monks, in the fight between Liu Kang, Kung Lao, and Goro, Johnny intervenes and finishes off Goro. This is both a mirror of his rivalry with him, and a nod to the final scene of the Cage vs. Goro battle in the first movie.
His first Fatality in the game has him transform into a clown who uses a prop gun to surprise his opponent... then use said gun to blow off his head. Just like The Joker's Fatality from Mortal Kombat vs. DC Universe, except now with that pesky T rating out of the way...
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.
In 4, her facial features are modeled after Talisa Soto, the actress who portrayed Kitana in the theatrical adaptations.
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 very similar to Superman's Heroic Brutality in MK vs DC, but with a decapitating kick at the end.
Kung Lao's weaponized hat gimmick was inspired by Bond's famous villian Oddjob.
Noob Saibot's 9 reveal trailer uses Ermac as his tag-team partner. This, plus his fighting style, seems to reference Annihilation, wherein Ermac spawned Noob to double-team Sonya.
In his Arcade Ladder ending, he makes a deal with Havik from Deception so that he can take over the Netherrealm. This could be a reference to how Havik started out as an alternate design for Noob named "Skab".
Noob's fighting stance in 9 is the same as Sub-Zero's in the first two games and Mythologies, referencing his status as the original Sub-Zero.
Noobs Player 2 coloration for his MK 2 costume turns his shade into Smoke, referancing their team in MKD.
Smoke's 9 chapter has him spying on Shang Tsung and Kano behind a tree in the Living Forest, much like he did on the player back in MK2.
In his Mortal Kombat 3 ending (as Human Smoke), it says he vanished into the Living Forest to study the techniques of his rivals.
Cyrax and Sektor seems to be ripped right out of Predator. If you ever had doubts about this one, Cyber Sub-Zero from 9 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.
Cyrax and Sektor were called "Mustard and Ketchup" during development. In Deadly Alliance, Cyrax has a combo named Mustard and another named Ketchup in reference to this.
In the cartoon adaptation, Mortal Kombat: Defenders of the Realm, Cyrax and Sektor were respectively shown to be Asian and Black before automation. Later games (such as Cyrax's ending in Gold and the showing of Cyrax and Sektor's human forms in 9) reveal that the reverse actually applies within canon.
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? Remind anyone else of 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 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.
Stryker's design in 9 serves as a visual update to his old look from 3, but also has some elements from his incarnation in Defenders of the Realm.
Overall, Stryker's design has him resemble Woody Harrelson to a good degree.
Ermac's Arcade Ladder ending in 9 reveals that one of the souls within his body is that of the late King Jerrod of Edenia (i.e. Sindel's husband and Kitana's father), who takes control of Ermac's body and returns to rule and protect Edenia alongside his family. This is a clever and very, very subtle nod to him being often paired up with Sindel in Ultimate Mortal Kombat 3 and Mortal Kombat Trilogy during Endurance matches.
Also in 9, Ermac is the only male "ninja" not in the first two games (excluding Cyrax, Sektor, and Cyber Sub-Zero) to receive a Klassic costume. This is a meta nod to the famous rumor that spanned the character in the first place.
If he gets knocked off Raiden's Sky Temple (introduced in Deception/Unchained and also used in Armageddon) and sent plummeting to his death, he's got two words for ya: "SUCK IT!!!"
Li Mei might have started as an Expy of Mileena, with her general appearance, use of Sai as weapons, and color scheme. From Deception onwards, Li Mei was revisited, and now has a notable smaller physique, uses a sword instead of Sais, and wears a suit of armor in battle.
In Mortal Kombat: Conquest, there was a character called Master Bo. Bo 'Rai Cho is clearly a reference to this man (with the other two syllables in his name forming a pun on borracho, the word "drunk" in Spanish).
He is a tribute to Carlos Pesina, the guy who did some of the MOtionCAPture for Deadly Alliance.
One of Kenshi's combos is named "Blind Justice", a reference to comic book hero Daredevil, a likely inspiration for the character.
Kenshi also draws heavily from Zatoichi, the blind swordsman; one of the main differences between the two is that Kenshi wears a blindfold.
During 9's story mode, Kung Lao faces off against the tandem of Quan Chi & Shang Tsung, the titular Deadly Alliance. Quan Chi even remarks that Kung Lao doesn't stand a chance "against this DeadlyAlliance".
The narration in Sub-Zero's Arcade Ladder ending uses the name to refer to Subby & Scorpion.
Lex Luthor's arcade ending in MK vs DC uses the term when he and Quan Chi join forces.
Bonus Challenge N° 34: Isn't This Marvellous (A match where you tap the screen repeatedly to fight.)
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.
If Stryker finishes Freddy with his Secret Fatality move, Freddy will have a bomb in his body and will explode, much similar to the ending of Freddy's Dead.
The stage Fatality for the city stage (having the opponent run over by a car) bears a striking similarity to the ending of the fourth Final Destination movie, 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. It's also a Call Back to MK 3 and its variants, where the subway stage and its fatality made their debut, only now it's much gorier.
In Kitana's Arcade ending, the three Edenia women characters are 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.
The new Test Your Strike minigame has a concept similar to the test given to Frank Dux in Bloodsport, where he had to break one brick out of a pile.