In this trailer you can see him adjusting his dislocated jaw.
LQ-84i's existence. A sentient AI weapon ordered to "defend the freedom of Abkhazia". However, it will be mind wiped at the first sign of questioning orders. Being an AI, the blade-wolf body isn't the important thing for it. If its memory is wiped, all of its experiences and learning will be lost. The chassis and neural net could be trained again, but it would never be the same intelligence. Having its memory wiped would be the same as death.
Some of the members of the Winds of Destruction, namely Monsoon and Mistral.
While not as immediately terrifying as the others, Sundowner can be pretty scary too, mainly the sheer, unadulterated glee he shows when he gets into a fight and his ungodly creepy Slasher Smiles.
The "Make it Right" viral ad campaign, a series of live-action trailers depicting Raiden undergoing surgery and experiencing various flashbacks. The disturbing imagery is what makes these ads Nightmare Fuel.
The whole encounter with Jetstream Sam during the prologue chapter. Sam stabs Raiden's eye out and slices off his arm, then the game screen becomes screwy and static-y as Raiden is struggling to move and has incredibly low health, and Sam slowly creeps up on him...
Senator Armstrong after activates his nanites. His eyes turn red, his arteries bulge out and cover his body, and every time he needs to deliver a haymaker or gets hit by Raiden, his skin turns a mechanical gray for a second before going back. After getting used to thinking of him as a politician in a suit, it's rather freaky to see him reveal himself as something akin to a more obviously inhuman cyborgs. Unlike most, it's not Cyborg tech but Nanomachinesnote Son. Even worse, if you look closely at his skin near where the greyish color ends, you can see red and veins on his skin. This can have the effect of looking like blood, almost as if the Nanomachines are tearing the armor through his skin, then regnerating him at high speed.
The rooms full of human brains placed into cyborg casings in the third and fifth chapters. They're brains stuck into little casings with just a pair of separate eyes and a dangling spine like device. The still living brains are terrified in this state, and when you enter a room full of them, they all stare at you at once. The fact that these brains once belonged to kidnapped children makes it all the worse.
In the Denver server room even more brains are shown, and Sundowner even strokes one as it undulates in muted terror.
Raiden standing over the corpse of Senator Armstrong after he ripped his heart out and crushed it is rather haunting of what it implies for his future. Raiden has a Thousand-Yard Stare with blood all over his body, clearly exhausted with all the killing and destruction he has had to cause and witness. He spoke of enforcing justice but knee deep in bodies Raiden can't help but feel Not So Different from his enemies.
Each one of the bosses is dispatched using a Zandatsu attack, meaning that they get diced to tiny bits. But then, they make dying codec calls. Despite being literally diced to tiny pieces, they are still alive, at least enough to make their last words.
If it's any consolation, Wolf was an AI, as opposed to the somewhat human Winds of Destruction.
They weren't necessarily alive. There are ghosts in the MGS universe.
Performing Zandatsu on Senator Armstrong. While it is very much awesome, you were previously ripping out fuel cells from cyborgs. The final battle has you ripping out someone's nanomachine-laced heart and crushing it while it still beats.
How Sam loses his arm. He slices off Armstrong's hand, leaving a crude, black-armored point. Armstrong knocks him to the floor and drives the sharpened point through his shoulder. The normally cool and collected Sam has a look of absolute horror on his face, and there's a shot of the arm twitching in its death throes and going limp.
The Mastiff, an ape-like Unmanned Gears. Mix that with a Blackout Basement level in the underground railroad in R-03, and you're in for a pretty scary experience.
Those enemies get a mention on their own because of how vicious and animalistic they are. Not to mention they're the Demonic Spiders of the game. And on Revengeance Mode, you have to fight one of them right near the start of the very first mission. Have fun.
Cyborgs and their associated weapons must be pretty terrifying to unaugmented, squishy humans. Take President N'Mani's kidnapping, for example. Sundowner hacks his guards into pieces while grinning, then picks him up like a ragdoll as he tries to escape his burning limo. Sundowner then ties him up and tortures him by pressing his high-frequency machete into N'Mani's neck, which is not only switched on, but also extremely hot. You can hear and see N'Mani's blood and flesh sizzling. The fact that the first thing he does after being cut loose is hold his neck closed and tell Raiden not to worry about him is a pretty awesome moment, when you think about it.