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Nightmare Fuel: Knights of the Old Republic
In the first game, the first time you see Malak without his jaw prosthesis.
The first two stages of Knights of the Old Republic II: The Sith Lords make up an exercise in creepy. In the optional prologue, the player controls T3-M4 on the shattered wreck of the Ebon Hawk, the only other occupants of which are another droid, one nearly-dead Jedi, several corpses, and something in a sealed cargo room that won't stop banging on the door. This is eerie enough, but when the player finally takes control of the main Player Character, it's to regain consciousness on a remote mining station and discover that someone or something has systematically crippled the station and murdered everyone else there while you were unconscious. Right around the time the tension is at its highest, the PC meets the HK-50 assassin droid responsible... and, although the extensive dialogue that ensues makes it abundantly clear what went down, the PC isn't able to do anything about it until quite a bit later.
"Mocking Query: Coorta? Coorta? Are you dead yet?"
Just the thought of Peragus is scary enough. You're on a mining planet and there's almost no way to escape until a ship appears...only it's full of assassins and dead people, with a powerful Sith Lord having done the killing. Escaping is basically going through a minefield. So there's almost no way out. It's definitely like something out of a horror game.
From both games, Korriban, though in very different ways.
In the first game, it's a small colony world with a Sith academy. The player is required to explore the tombs of dead ancient Sith, which even the powerful Sith at the academy are afraid to enter. In one, you have to have a conversation with the Force-ghost of a long-dead Sith Lord. In another, you're captured by a completely insane psycho who asks you a series of questions, and if you get them wrong he'll torture you with lightning. If you get them right? He'll torture someone else instead. This is added to by the fact that the Sith at the academy are casually cruel, to the point that they'll torture applicants to the academy until they collapse, leave them for dead, and then not even let them into the academy. Nearby, you can explore a cave filled with giant flying reptile things which are more annoying than scary, but also in the cave is a terentatek (think a rancor, but covered in spikes and resistant to Force powers). In one of the tombs, there are two more which you have to fight at the same time. And one of them can kill your entire party if you're not very careful.
Which also goes to show just how badass Revan is. During the Great Hunt, it took three Jedi to kill a single Terentatek and having any less than three Jedi attack one is suicide. Then you come along and kill three at once, all by yourself, and two more (at least, assuming that is what the thing in the Lower Shadowlands on Kashyyk is) with your party assisting you.
From the second game, the academy is abandoned. The door to the colony is collapsed, but there's clearly a reason you landed in the Valley of the Sith instead of there. There are decaying bodies lying around. The person you went there to find is lying dead inside a torture cage. And then you're attacked on the way out by Darth Sion. And before you even enter the academy, you're attacked by invisible giant reptiles.
Said giant reptiles don't attack you unless the player tries to loot the random corpses laying randomly on the ground. Because they are only invisible, this means they're always there, watching you go about your merry way.
Every one of Sion's appearances. Especially the medical bay log on the Harbinger that has the doctor going along normally before stopping to look at something offscreen with shock, then the camera shorts out and you hear screaming followed by Sion's deep, gravelly voice saying "I have come for the Jedi."
Though you're on a safe side, while your on the surface of Telos you can look towards the containment field on the edge of the map. The sky is black and you can see lightning. It makes you wonder exactly what the sections of the planet that haven't been restored yet look like...
Much like the above, Malachor V wasn't always a barren, twisted rock. You did this to it, Exile.
The Hrakert Rift station on Manaan in the first game. Full of insane Selkath that try to rip you to pieces inside, surrounded by firaxen sharks that try to rip you apart outside. The outside is actually worse because you can't see them until they're practically right on top of you and your targeting system picks them up. And there are more beyond the edges of the map. Not to mention that you can see the massive one hovering by the bridge, ready to eat you if you try to cross over to the Star Map before you've done something to get rid of it, either by destroying the kolto filters or poisoning the water.
Not to mention the fact that even a scratch from these beasts will turn someone into a rakghoul.
Encountering the freshly bitten victims is worse. Listening to them scream as they change into rakghouls? Even worse.
The captive Jedi in Malak's command room — dead, but not released to the Force, and serving as battery cells for Malak whenever he needs a Force boost.
Darth Nihilus. He devours entire planets and doesn't care who he devours. If not for the Exile, he would have devoured the Jedi, then the Republic, and all sentient life in the galaxy, including the Sith. What makes it worse is that he speaks one of the few languages in the game that isn't subtitled. It's hinted that he is speaking the language of the True Sith, but if that's the case, how did he learn it?
His outfit is pretty scary too: totally black robes and a mask made of bone. It only makes it scarier when you hear from Visas that he doesn't have a body because he's devoured himself and all that remains is his essence, using the Force to keep his physical shape.
The way he speaks is especially creepy. Even with the weirdest of alien languages, they at least sound like speech, or at the very least, something natural. Nihilus? His voice is like a warbling, strange hiss that doesn't sound even slightly natural. If seeing him alone was not enough to convince you that this guy was bad news, hearing him speak surely will.
Canderous' insight on the unknown planet.
Canderous: This world is... odd. It looks like a battlefield, but the environment is lush and green. Whatever happened here was a long time ago. I've seen many strange worlds in my time and this is the strangest still. (nervously) I don't like this place. Something happened, or will happen, and I don't like it. We should get out of here as soon as possible.
You know a place is dangerous when even Canderous is feeling unsettled.
The cut-scene with Darth Sion beating up Kreia. Her muffled scream, watching Sion beating up an old person and the implied rape afterward.