The executions, all of them. Have fun trying to sleep at night after you watch one of these. Let's break them down, chapter by chapter:
The first execution we see in the game, "Blast Off!". The victim starts off tied up and blindfolded, struggling as he tries to free himself, only to be shown screaming as he is put into the small space shuttle. It's sent into space up toward an incredibly creepy-looking sun and moon, then falls back down to the earth again, upon which the shuttle opens to show only his bones left, and then there's the shot of Monokuma just laughing... The fact that we don't know who it is initially dampens it somewhat, but it gets worse to watch it again upon knowing who it was: the headmaster, Kyoko's father.
If the relevant pages in the Reload book and the implications made by the early trailer are anything to go by, this was originally Leon's execution (though he may have simply been a placeholder, as Leon was the first male character designed and was the template for all the others). Also, in other illustrations the rocket doubles as an iron maiden.
Chapter 1's execution, "The 1,000 Blows". There is a great reason it is the above picture. Leon Kuwata, the Ultimate Baseball Star, is the first culprit. You first see a chain close around Leon's throat while he reaches out for help, and then it starts dragging him very quickly along the ground while he's desperately clawing at the chain the whole time. It takes him past a door that ominously closes, only it turns out the chain is dragging him to a batting cage. Leon isn't even given a fighting chance; after the chain drags him to the signpost inside the batting cage, more chains appear encircling around just the right places on his body so he can't move his arms. Now why would Monokuma not want Leon moving his arms? So he can't raise his hands to defend himself when the pitching machine beats Leon to death by shooting baseballs at him! It doesn't even have the mercy of killing Leon right after the machine starts; you have to watch the machine moving up and down Leon's body from shoulders to toes and back again, while the music track conveniently plays the "wo-wo-wo-wo" voices part of the song during that part, and then one final shot of Leon looking scared out of his mind right before dozens of baseballs hit him in the face and that finally kills him. And when the machine finally stops firing, you have to watch the baseballs just slowly rolling away, covered in blood, as Leon's mangled crushed corpse hangs there limply. Also, his silhouette in the ball-rolling shot looks like his feet are off the ground, so it's possible the chain around his neck was strangling him throughout just to top things off.
This execution was so brutal that it ended up censored in The Animation (in the original broadcast, but not the DVD or English dub) so as to not show the baseballs hitting Leon or the bloody baseballs rolling away from Leon's dead body afterwards.
Chapter 2's execution, "The Cage of Death". This time it's Mondo Owada, the Ultimate Biker Gang Leader, being executed. Mondo is tied to a motorcycle by his arms, with Monokuma driving it. Monokuma drives the motorcycle towards a "motorcycle death cage", but Monokuma ejects from the vehicle before Mondo is taken inside the cage. The reason why becomes obvious: Monokuma then proceeds to do a hula dance that speeds up the cage to absurd extremes, with Mondo having a freaked-out look as his eyes look dizzy, and finally Monokuma speeds up the cage to such ludicrous speeds that Mondo is turned into butter, which Monokuma then puts on his pancakes and eats! This one is mitigated slightly, though, since Mondo makes no attempt to escape the vehicle he's tied to, even giving Monokuma a "dude, really?!" look as Monokuma ejects, and you don't actually see Mondo turned into butter, you just see the lone motorcycle left on its side with no occupant.
Kiyotaka's reaction afterwards is equal parts this and Tear Jerker. That scream really hammers in that he just saw his best friend horribly executed in front of him. Trying to imagine things from his perspective is just horrifying.
What's especially terrifying is that this type of death is entirely plausible in Real Life. It's possible to exert enough force onto a human body to the point where they're crushed to a pulp (his consistency would be more akin to salsa than butter, though). Granted, Mondo would've died long before being liquefied since the immense pressure on his lungs would've caused him to suffocate. That, or death by internal bleeding due to his blood vessels rupturing as well. Either way, it's a horrible way to go.
Chapter 3's execution, "The Burning of the Versailles Witch". It's Taeko "Celestia Ludenberg" Yasuhiro, the Ultimate Gambler. In a corruption of her dream, she stands surrounded by a cardboard castle and is set to be burned at the stake, a slow and agonizing death that would give anyone nightmares at the thought of it. Only, this is the dramatic kind of death Celeste wants... so Monokuma intentionally pulls a bait-and-switch and sends a firetruck to put out the fire. Except the firetruck rams her to death! The only mercy you're granted is that you're not actually forced to watch Celeste being crushed, since the camera at that point is from Celeste's point-of-view so you only see the truck and hear the sound effect.
Chapter 4's execution, "Excavator Destroyer". You might wonder how it would be nightmare fuel to use a bulldozer to crush Alter Ego, an Artificial Intelligence, to non-existence. Monokuma manages it; his bulldozer repeatedly strikes Alter Ego's laptop causing damage while Alter Ego looks frightened, and then it speeds up and crushes the laptop into a ball with Monokuma's face on it. And based on Alter Ego saying earlier that being in Makoto's jacket "tickles," he felt the whole thing.
Chapter 5's execution, "After School Lesson". In the bad ending, it's Kyoko Kirigiri being executed. Her hands are pinned underneath the top of a desk so she can't get up from her chair, and she's forced to watch a puppet Monokuma teaching a lesson on the chalkboard about a crushing machine. Only the crushing machine is real, and the chair is on a conveyor belt moving Kyoko towards it. So Kyoko has to listen to the huge block repeatedly crashing down behind her, and you see her shoulders heaving slightly, and her face turns blue out of horror: Kyoko Kirigiri, the eternal stoic, has finally been broken and made to feel fear. Mercifully, the game fades to black at the moment when the huge block actually crushes poor Kyoko to death, but you can still hear it...
If you-as-Makoto choose not to get Kyoko executed... Makoto himself is slated to go through the "After School Lesson". Except Alter Ego, who uploaded himself as a virus to the school's network before his execution, saves him at the last moment, and later the living Kyoko finishes the work. It's still fucking scary.
And now with Cyber Danganronpa VR: The Class Trial, you get to experience this execution through the eyes of Makoto when Monokuma decides to end the demo by executing him. This time, however, he's facing the machine, and Alter Ego isn't here to save him...
Finally, the last execution in the very end: "The Ultimate Punishment". Yeah, you don't get to feel sorry for the victim because it's Junko Enoshima, the Big Bad who was behind Monokuma and was to blame for the whole plot in the first place... but still, she willingly subjects herself to all the aforementioned deaths! Plus "Blast Off!" from the game's beginning (where the victim [all but stated to have been Kyoko's father the ex-Headmaster] is trapped into a small shuttle and shot into space — and brought back, which destroys his body save for his bones). And she lives through them until "After School Lesson", and enjoys them thoroughly due to her fetish for despair, smiling madly until almost the very end. Meeeep.
Junko's face just before the execution, as she willingly reaches out to press the button...
Something that sticks with you is the way she stops smiling just before the crusher slams down for the last time. You can almost hear her thinking "Wait—"
Another thing that makes this execution even worse. It's implied this was the execution the Mastermind intended for Makoto had he failed to defeat her.
Sayaka's execution would've had Monokuma place her on a stage, promising a perfect idol singing performance, complete with a meter to "score" her. Being the Ultimate Pop Sensation, she naturally would've done well. However, just before the meter reached full, Monokuma would've destroyed it. This would've triggered the failure condition and caused a giant beartrap-looking contraption to slam shut, presumably bisecting her. And this could've happened if she successfully killed Leon. So in this scenario, Makoto would've had to personally expose his closest friend's crime, including her lying and trying to frame him, before watching her die.
Aoi's execution would've had her placed in a water tank with Monokuma dressed as a magician. Think she'd be sentenced to a death by drowning? Monokuma is nowhere near that merciful. Instead, he would've placed a curtain over the water tank, lifted it back up to reveal Aoi surrounded by sharks, then covered it again, and lifted the curtain once more to reveal she'd been eaten.
Byakuya's execution would've had Monokuma drop him into a trash can in a place that looks like hell. It's here that Monokuma, dressed as an elementary schooler, would then start viciously stoning him. Byakuya would've managed to escape, but he'd then end up in a snowy wasteland. It's here that he would've died from his injuries and exposure to the cold.
Toko's execution would've had her thrown into a dark room, with Byakuya in the distance. She would've run to catch up with him... only for a giant steamroller to drop between them and chase her, ultimately crushing her to death.
Hifumi's execution actually appears in the manga adaptation of the demo: he gets caught in a fight between his favorite character Princess Piggles and Monokuma, taking laser blasts from both of them, before getting finished off by "instant death" beams from both of them. His corpse ends up so charred that the only way he's recognizable is due to his fat.
Any time Junko appears while wearing the mask she used to hide her identity is fairly creepy or unsettling. The first time is absolutely terrifying as it's her sneaking up on Makoto as he reads something that could clue him in to the truth and clubbing him with a piece of lumber. Sure she's just knocking him out so she can hide the evidence, but given the kind of story the game's telling it can fill a first time player with the dread that they've been playing as a Decoy Protagonist this entire time and that Makoto is the next victim.
The bad ending that you get after Kyoko's execution may not seem so bad at first glance, but Fridge Horror kicks in when you consider this: While the remaining students (Byakuya, Makoto, Yasuhiro and Aoi, and Toko was with them but she died a while ago) have stopped killing each other — they still never leave the schooland have grown to adulthood totally isolated from the rest of the world. Worse still is the mystery behind Toko's death and the fact that there are three children in their group shot. Considering that Aoi is the only girl remaining, that means she gave birth to all three of them (probably; it's never stated when Toko died). And the four remaining kids are going to grow old and die, still just the four of them, and their children will be subjected to the same destiny, lonely forever...
Monokuma revealing to the kids that they're here... forever.
"Ah, now then... regarding the end date for this communal life... there isn't one! In other words, you'll all be here until the day you die! Such is the school life you've been assigned."
"No matter how much you may yell and scream for help... help will not come."
In Chapter 6's trial, Junko's initial appearance is shocking enough... but then she starts rapidly changing personalities, each one freakier than the last. The really cutesy one and the one where she covers her own face with Monokuma and speaks through him are particularly jarring. And then, once you reach the final discussion, she assumes a completely neutral, blank expression, and tells them of what has happened to the world and that defeating her and leaving the school means certain death. This, combined with the horrified expressions on the students' faces, is probably the scariest that Junko gets to be.
Something about the way corpses are rendered on the overworld is especially unpleasant and skin-crawly. They just seem way more detailed and shadowed than the rest of the game in a way that makes them feel absolutely wrong.
The premise of the game is incredibly horrifying. You're stuck inside of a school and the only way out is to kill someone. And even if you yourself choose to go the pacifistic route of rather living in the school than committing a crime, you still have to constantly worry about the other people. At any moment, any of them could snap and kill someone, or even you.
The murders get progressively nastier as time goes on.
Sayaka (Yasuhiro in the demo): knife to the gut.
Chihiro: dumbbell to the skull; later crucified.
Kiyotaka and Hifumi: brains bashed in.
Sakura: ingested poison.
The Masked Would-Be Assailant (actually Mukuro's body): found in the garden, and gets her face blown off when Jill tries to unmask her.
Hell, the fact that one high-school aged girl, armed with nothing but her charisma, managed to nearly cause the end of the world out of sheer sadism.
Classroom 5-C. Imagine playing the game blind. You've gone through four class trials and, sure, the executions have been fairly unsettling and the murders are pretty gory but, on the whole, the game's pretty tame (especially since all the blood at this point has been neon pink). Then you get to exploring the fifth floor, you've come to expect a few unique rooms as well as two classrooms and you expect the same here. However, at some point, you notice a door labelled Classroom 5-C. A little surprised at the sudden additional classroom, you enter it to see what's inside because there's gotta be something in there, right? The classroom loads up to reveal a bloodied mess with all the tables and chairs toppled and sprawled along the floor alongside multiple chalk outlines of bodies. The real kicker's the fact that the blood in this room isn't the neon pink that you see everywhere else but a dark red. Eventually, Monokuma comes in to tell you that the room was already like this before the killing game started and that he deliberately left it like that as a clue (which is why the blood is red, it's dry). The worst part is that the game never actually reveals what exactly happened in that room (in fact it's never even really mentioned much outside of its initial reveal). You do eventually find out what happened in there in laterinstalments but the fact that room is just left there without a conclusive explanation is unsettling at the very least
Due to the liberty of more animating department, they actually made Celeste flipping off angrily in the 3rd chapter look a lot more terrifying. If one pays attention, one can see that the whole thing freaked out even Monokuma.
Syo can be pretty scary too, in the anime versions of her angry poses, particularly the one where her skirt flies up behind her as she brandishes her scissors at Makoto.
The English lyrics of the "Monokuma Ondo" song. It doesn't start off too bad, talking about how the world is a just place and how it's easy to see through people's emotions. Then it all gets creepier as it starts talking about happily devouring each other as multiple Monokuma's rise to center screen to dance in happiness while confetti rains down around them and a giant Monokuma statue. Jesus Christ.
In If, the rather graphic description of Makoto being stabbed by a Gungnir Spear can be this, considering how fond the player would probably be of him from the first game. Just when you think it can't get much worse, Monokuma (who you know is Junko) being his (her) bastard self and making all sorts of sexually-charged assumptions of what Mukuro will do to an unconscious and dying Makoto to try and distract her (compared to the outlandish commentary he would make in-game, these are more flat-out allusions to rape, due to Junko's knowledge of her sister's crush on him). Oh, and let's add in Jill's commentary about it too, the murderer who got her "bloodstain fever" upon seeing the bloody scene for good measure.
Towards the climax of If, the mastermind threatens to reset the game by erasing everyone's memories all over again — and Mukuro's punishment for turning on her? Getting to play as herself, but with Laser-Guided Amnesia, so that she doesn't remember her talent or being part of Ultimate Despair. This way, even if she didn't get killed or become a murderer herself, she'd still eventually discover the Awful Truth and risk having everyone turn on her...
In its earliest version, the game was known as Distrust, and it was apparently going to be a flat out horror game instead of the black comedy it ended up as. Trigger Happy Havoc ended up with plenty of Nightmare Fuel, as this page makes clear, but at least the kids were never subjected to things like the blankly-staring decapitated head and severed hand of one of their classmates, left in a plain cardboard box for any one of them to find. The implication seems to be that the victim — possibly Junko — was forcibly shoved into a guillotine... by Kyoko, Toko, Leon, and an unidentified fourth student who might be Yasuhiro. That's right — at least one route involved a gang killing. And if Leon's early execution is anything to go by, you could only expose one of them.
The final game's school is relatively intact. Distrust's school is a blood-soaked wasteland, and Class 78 is on a sadistically short time limit of seven days.
As more information comes to light it turns out that Junko being decapitated wasn't because she was the victim of murder... but because she was executed for committing it! But if that's not bad enough, consider the image right before the guillotine was shown, with silhouetted people all smiling madly and reaching out to her! It's highly possible that instead of getting dragged to their death by chain, the guilty students were to be seized and forced to their deaths by the innocent students a la lynch mob. Also, if one was to look closely (as if you would want to) below the girl (now most likely, Kyoko) you can see an object which largely resembles a bonesaw... and considering the lead girl/Junko of the group is holding something in her hand, the implication of what they did to the poor girl is more than just a 'little' unsettling...
At least one of Kyoko's deaths involved Kazuo (Leon) getting his hands on a bunch of spears and impaling her on every single one. And you thought Mukuro's death was bad...
And his execution, terrifying enough in the final version, was even worse. Highlights include Kazuo/beta!Leon spewing gallons of red blood and his beaten corpse not being as obscured by the shadows.