Shao Kahn's Hara-Kiri. He throws his hammer up into the air, strikes his signature hands-on-hips pose, and waits for the hammer to come down, upon which it hits him on his head, causing it to explode. Then the body drops to the floor.
Most of the Hara-Kiri's are absolutely hilarious. Special note goes to Sindel, who appears to botch a backflip and breaks her own neck when she tries to land, and Dairou, who somehow snaps himself in half like folding a piece of paper.
Liu Kang's second fatality, when performed against himself or any of the female characters, can be absolutely hilarious.
The Kollector's Edition contains a trading card video for Johnny Cage. His enemies are listed as "Shang Tsung, Goro, Movie Critics".
In konquest, before an optional fight with Scorpion, a yes/no prompt pops up saying ""GET OVER HERE!!" Will you go over there?"
There is something amazing about how Konquest mode has a dedicated button for punching people. Just walk up to anyone you like and straight up cold-cock them. Some NPCs go down in one shot, others simple whine and complain about you hitting them for no good reason ("Are you insane?! I am not the enemy, Shao Kahn is!") or threaten you if its someone like Shao Kahn himself. And other times they'll block it, then complain or even hit Shujinko right back and leave him flat on his ass. The funniest goes to Sektor, who is just standing around in Edenia minding his own busines, glitching out due to damaged parts. hit him once and he complains as such:
One side quest in Konquest Mode involves a teenage boy who hires Shujinko to scare his grandfather. You accomplish this by slowly walking up behind him and punching the old man.
In Konquest Mode, Mokap's goofy walk in Orderrealm.