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 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".
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.
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.
In Kitana's Arcade Ladder ending, three Edenian women (Kitana, Jade, and Mileena) 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 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.
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 have her jump into the fray (and off of his shoulders) to help out.