Most of the Hara-Kiris are absolutely hilarious. Special note goes to Sindel, who botches a backflip and breaks her own neck; and Dairou, who somehow bends backwards and snaps himself in half like folding a piece of paper.
Scorpion has a good one in that it defies all expectations; rather than doing something like setting himself on fire or using his spear to rip his head off, he simply just kneels down... and snaps his own neck.
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, Havik wants Shujinko's help to convert three Orderrealm soldiers to Chaos, under the guise that he will teach him the ways of Chaos as a reward. Once Shujinko actually does the quest and returns to Havik, he admits to lying and intends to kill Shujinko. When Shujinko wins their fight, Havik proudly proclaims that Shujinko has learned the ways of Chaos. Shujinko, obviously ticked, asks how is that possible if he tried to kill him, and Havik explains that Chaos is basically learning through experience to defend himself rather than being told how to do so. Shujinko thanks him for the mock battle, but Havik tells him that he would have killed him if given the chance.
Ironically, Havik is one of the few characters in Shujinko's journey who was completely helpful, even in his betrayal, he helped him.
In Konquest, before an optional fight with Scorpion, a yes/no prompt pops up saying ""GET OVER HERE!!" Will you go over there?"
"Would you care to come back later for some Nikko stew?" Explanation (In Konquest, one of the sidequests in the Earthrealm village has a woman ask Shujinko to find her dog. Talk to the local butcher, and he reveals that he slaughtered the dog, unaware that it was somebody's pet, and gives you its meat. When you take the meat back to the woman, she's briefly distraught, but grudgingly realizes that it's not a total loss, and after paying him for technically doing what she asked, she asks Shujinko the quote.)
There's something amazing about how Konquest has a dedicated button for punching people. You can just walk up to anyone you like, and flat-out deck them. Some NPCs go down in one punch, others simply 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 it's 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 business, glitching out due to damaged parts. Punch him and he complains as such:
One sidequest in Konquest involves a teenage boy who hires Shujinko to scare his grandfather. You accomplish this by slowly walking up behind him and talking to the old man. The boy pays you and offers to pay double if Shujinko does it again, but the second time you do it, the old man dies from a heart attack in shock.
One sidequest in the Earthrealm village has Shujinko looking for proof that oni exist for a brother and sister. When night falls, an oni appears in the village, doing the same goofy walk down the street. And you have to punch him out to get a tooth to show the siblings!
Triggering a Death Trap in the first round is this, in and of itself. You get to send your opponent falling to their death, crushed by machines/rocks/etcetera, or horribly killed otherwise, and they're up and fighting again the next round.
When you fail Kenshi's basic low attack training in Konquest, he says this:
Kenshi: I could do this when I was 10! Repeat your training!
Puzzle Kombat, the Super Puzzle Fighter II Turbo-style minigame where the characters take on a Super-Deformed appearance and engage in more slapstick violence with each other, such as uppercutting an opponent and sending them flying offscreen for a few seconds, or giving a present to your opponent, which then explodes in their face.
And then there's the end screen and its upbeat acapella song.
Some Citizens of Choasrealm and Netherrealm have their speech reversed. Returned forward provides lore and forshadowing, but also funny messages: