This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Borderlands
Sledge's Safehouse is extremely disturbing the first time around. "THEY GOT ME" written in blood on the walls, presumably written by the victims in their own blood at the command of their captors, bodies chained up all over and strung up like chandeliers leaking pools of blood, huge blood splatter everywhere, bodies stuck to the walls and ceilings via steel rods jammed through their eyes, a room with an armless body along with several dismembered appendages and a body stuck up on the ceiling, a small "Colosseum" where victims were presumably forced to fight the cannibalistic Psychos for sport, and on and on. In many cases, fresh blood still drips down from strung up bodies.
The Badass Psycho can be quite disturbing when you first encounter him. You're fighting a group of bandits, when all of a sudden, a pale-skinned mountain of a man with a right arm as long as his entire body charges you and starts swinging away with a buzz-axe. Even worse, their left arm is atrophied, as if someone sucked the muscle and bone out and injected it into the other arm. Also, they seem to be even more crazed than normal psychos, to the point of being unable to talk, instead simply growling and screaming.
Another area near Patricia Tannis's place has a body held out over the edge of a cliff by two rods. He's tied by his neck to the top and by his feet to the bottom, plenty of rope between his body and the rods, and with a brace on his neck so he doesn't actually suffocate. When you go up there, you find three bodies impaled on steel pipes to a wall, with dart boards visible behind them, and barrels under them to collect the blood. One barrel is on fire. So you go to the strung up man, and as you do, a flock of Rakks attack you. So apparently the man was put there to be fed on alive.
In Krom's Canyon, you will occasionally see natural bridges of earth connecting the two sides of the canyon. Several people can be seen hanging by their necks from them, hands bound behind their backs. One of them was on fire.
General Knoxx's descent into nihilistic despair is played in-game for laughs, but when the reality of it sinks in, it's quite chilling. The sheer resignation of Knoxx to his situation, the fact you literally interrupt his efforts at committing suicide, the fact he insists you ought to just blow Pandora up and kill everyone on it when he dies...
By extension, the whole "Secret Armory of General Knoxx" storyline for what it reveals about the utterly crapsack nature of the whole universe. Gross incompetence, corruption, nepotism... It's an awful stew of everything that could go wrong with the government and big business, to the point where the Vault Hunters, who are seen In-Universe as bloodthirsty anarchistic psychos who simply kill everything in sight for profit and pleasure, really do look heroic by comparison.
Secret Armory implies that there are worse places than Pandora that Atlas personnel can be assigned to.
In Claptrap's New Robot Revolution, fighting the Bandit-Traps becomes disturbing fast when one of their death cries is "Please... Just let me die". Suddenly it puts the Claptrap conversion into a VERY different light.
If you have a thing against giant hissing cockroaches or bugs in general, then the Scythids when you first encounter them in a tiny, hard-to-maneuver space is going to be fun!!!
Psycho zombies can be frightening if you don't finish them off once you knock them down. They get an insane speed boost, marked by their glowing eyes, allowing them to bolt right up to your face.
The elemental tech weapons all have unique death animations if they kill a humanoid victim with elemental damage. Explosion just blows them to bits, but the other three are much more disturbing...
Fire weapons engulf their victim in flames, who screams and flails in an attempt to pat them out even as they burn him into ashes.
Shock weapons make their victim stand up ramrod straight, twitching madly as the flesh melts off their skull, leaving two eyes staring at you from it. Then an eyeball pops out. Then a part of the skull pops off, exposing the brain. Then they fall over and their head explodes. In the sequel, they're merely vaporized, not that it makes it any better.
Acid weapons make their victim scream and wail as they dissolve in a splashing gush of green fluid. With Psychos and Bruisers, their mask gets left behind.
Crawmerax The Invincible. Holy mother of fuck, is Crawmerax the Invincible terrifying. The player is treated to a brief look at the guy as they enter Crawmerax's Lair (the loading screen), and the mere appearance of the dude is enough. A nightmarishly deformed Crab Worm-Tarantella-Walrus-whatever that absolutely towers over the player(s).
And then there's actually trying to beat the guy. Get close to him and he'll lunge and try to bite you. Go ahead, keep your distance — he'll start shooting out purple globs from his teeth that are composed of acid and will eat away at the fabric of your shields. You think you're able to avoid his glob-shooting? That's not even his worst attack. He'll burrow underground and then explode out at an unexpected point — unless you're able to avoid the blast radius or jump at the right time, when Crawmerax pops out again above ground, the sheer weight of him will send you flying.
His maximum is Level 72 — a full three levels above the set limit of 69...
Easily the most difficult boss in the game — even with four players he is tough. While he is not really invicible, by God, he's damn close.
Then the glitched ledge was discovered...and subsequently he's become a bit easier to beat.
The Drifters added in in the General Knoxx DLC. They're essentially giant spiders on tall legs that can shoot acid at you. To make matters they have no movement noise, meaning they can easily sneak up on you.