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, aka "The Space Journey". 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, aka Kirigiri'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. Also, in other illustrations the rocket doubles as an iron maiden.
Chapter 1's execution, aka "Million Fungoes". Leon Kuwata, the Super High-School Level Baseball Player, 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 so as to not show the baseballs hitting Leon or the bloody baseballs rolling away from Leon's dead body afterwards.
And then we have the beta version. Highlights include Kazuo/beta!Leon spewing gallons of red blood and his beaten corpse not being as obscured by the shadows.
Even Monokuma itself looks horrified when it's over (though whether this is genuine horror or mere trolling is unclear).
Chapter 2's execution, aka "Motorcycle Death Cage". This time it's Mondo Oowada, the Super High-School Level 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.
Ishimaru'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 liquified 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, aka "Versailles High Witch Hunt Stake". It's Taeko "Celestia Ludenberg" Yasuhiro, the Super High-School Level Gambler. She's all 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 Celes 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 Celes being crushed, since the camera at that point is from Celes' point-of-view so you only see the truck and hear the sound effect.
Chapter 4's execution, aka "A Dozer Master". You might wonder how it would be nightmare fuel to use a bulldozer to crush Alter Ego, who can't feel pain, 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.
Chapter 5's execution, aka "Detention". In the bad ending, it's Kyouko 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 Kirigiri towards it. So Kirigiri 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: Kyouko 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 Kirigiri to death, but you can still hear it...
If you-as-Naegi choose not to get Kirigiri executed...Naegi himself is slated to go through "Detention". Only that Alter Ego, who managed to survive its "death" via downloading its memory in the main network, saves him at the last moment, and later the living Kirigiri finishes the work. It's still fucking scary.
Finally, the last execution in the very end: "Super Duper Nasty Torture". Yeah, you don't get to feel sorry for the victim because it's Junko Enoshima aka 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 formerly mentioned deaths! Plus the "Space Journey" one from the game's beginning (where the victim [all but stated to have been Kirigiri's father aka 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 "Detention", and enjoys them throughly 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 Naegi had he failed to defeat her.
Also, related to the above... Here is a post that includes the plans for the whole cast's executions. Among them are: Aoi's ("Water Show Illusion", in which she's trapped inside a water tank and Eaten Aliveby sharks), Togami's ("Human ★ Disqualification", where a hobo-looking Togami is thrown into a place that looks like Hell and first gets stoned by Monokuma, then ends up Dying Alonein the snow) and Fukawa's ("First Prank Kiss", with her crushed to death by a roller after Monokuma mocks her Mad Love for Togami via making her believe he'd kiss her)...Wow.
Any time Enoshima appears while wearing the mask is fairly creepy or unsettling.
The bad ending that you get after Kirigiri's execution may not seem so bad at first glance, but Fridge Horror kicks in when you consider this: While the remaining students (Togami, Naegi, Hagakure and Aoi, and Touko 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 Touko'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 Touko 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.
"Eh— in addition... regarding the extent of this communal lifestyle... Itís going to be forever!! In other words, you are going to live here your entire lives! That is the school life we are assigning to you bastards!"
"Thatís right. It doesn't matter how much you shout. No help is coming."
In Chapter 6's trial, Enoshima'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 Enoshima gets to be.
Something about the way corpses are rendered on the overworld is especially unpleasant and skin-crawly.
Here's an article about Distrust, the earliest known version of Dangan Ronpa. The final game had its nastier moments, 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 Kirigiri, Fukawa, Leon, and an unidentified fourth student who might be Hagakure. That's right—at least one route involved a gang killing. And if Leon's beta 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.
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 beta's premise (called Distrust) was actually worse. The characters had merely 7 days instead of the indefinite entrapment and it can be assumed that everyone would be killed if a successful murder wasn't committed. The few deaths shown in the proposal were even more brutal, and the same can be assumed of the unknown executions.
The murders get progressively nastier as time goes on.
Maizono (Hagakure in the demo): knife to the gut.
Chihiro: dumbbell to the skull; later crucified.
Ishimaru and Yamada: 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 Syo tries to unmask her.
Kirigiri's death in Distrust, or one possible death. Somehow, Kazuo (Leon) got ahold of a bunch of spears and impaled her on every single one.
Dangan Ronpa If
In If, the rather graphic description of Naegi being stabbed by a Gungnir Spear can be this, considering how fond the 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 Naegi 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 her sister's interest in him). Oh, and let's add in Syo'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 SHSL 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...
Due to the liberty of more animating department, they actually made Celes 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 Naegi.
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.