Did you know, the character Rain (first introduced in Ultimate Mortal Kombat 3) is a parody of the Prince song, "Purple Rain." Its also nice to mention that he does wear purple, and his story was designed that he was an actual prince of the realm of Edenia.
Kano and Noob Saibot were originally meant to be in Mortal Kombat 4. However, due to Ed Boon wanting new characters. Reiko and Jarek were put in the game instead of the originals.
The character Ermac first started as a rumor in the original MK1, as the game have ERMAC (Error Macro), to make sure any problems didn't happen with the game. This spread wide rumor, that Ermac was another hidden character within the game, and even some skilled artists got a red palette for the character (http://img.photobucket.com/albums/v460/h...rmac.jpg).
The same thing happened with Skarlet, except as a coding glitch in MK II.
Noob Saibot is Tobias Boon backwards, he is also Sub-Zero's (MK II) older brother.
Cyrax and Sektor were once referenced as Mustard and Ketchup, and have some combos referenced in the 3D games (Deadly Alliance and Armageddon).
In the original Mortal Kombat, there was a glitch that allowed you to do Johnny Cage's fatality multiple times. This glitch was also referenced in MKII, where a fatality knocked off three heads instead of one. The creators also wanted Jean-Claude Van Damme to act as Johnny Cage for the first game, but was unable to due to busy movie work. Johnny's clothes are based off of Van Damme's movie Bloodsport.
In the Mortal Kombat: Shaolin Monks, when you perform the fatality on Goro, Johnny Cage stops you, and and finishes off Goro instead. This moment is homage to the movie, when Johnny Cage DOES defeat Goro.