This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Vault Hunters Wanted
Any of the fight scenes would count. The author takes a long time to vividly describe the injuries inflicted on both sides, with even minor scrapes being disturbingly detailed. A few notable examples definitely stand out though.
Marie Winter vs Krieg. The first one shows how Krieg hasn't changed at all during the 5 year absence, slaughtering a squadron of Bellum troops before taking her on. The second one has Marie Winter going Stalker with a Crush on Krieg, showing a disturbing obsession towards him that sounds suspiciously Yandere in style.
Major General Sine. He has eyes in the palms of his hands and using his two main eyes caused them to bleed. When he fought Maya one of his eyes is yanked out before being disintegrated into dust.
The Vault Hunters vs Doctor Suture. His Bloody Murder powers are played for their entire Squick value, along with Dion's plasma abilities.
The Vault Hunters vs Famile. There is no explanation to what exactly he is, and his dialogue is creepily ominous. Ironically, he actually gets a happy ending, having seperated his family from his assimilated body and being happily together.
Aurai vs Masher, or more specifically, what happens to him from her. Two arms ripped off, an eye gouged out, a roof collapsed onto his body, and being set on fire was what it took to be put down. It's still Nightmare Fuel just because of the vivid detail that is put into it.
The Vault Hunters and Lupus Cithara vs Elena Tear. Her original impression is The StoicDark Action Girl, but she turns out that she's a repressed Blood Knight who battles with a Slasher Smile and a transformation sequence eerily similar to Gaara's Shukaku transformation. When she fights, she either shreds people apart with her sword or drowns them in her water powers, showing no remorse for either of these actions. Even the narrators are scared of her, and with good reason.
The Vault Hunters vs Jackal Cash. He's The Determinator mixed with Combat Pragmatist, with his second fight being the prime example of this. He takes out Dion first, as he was the biggest pain in the ass for him, and then targets Saprus to be rid of his disease. The occult ritual that makes him immortal is just creepy icing on the cake.
Teresa Pangolin vs Gueule. Seeing the normally quiet, sweet old lady blow off the Grave Servant's legs and make him bleed to death is disturbing as hell, especially given how easily she did it. Even creepier: she acted completely calm and professional during it, like she had done this before.
Saprus, despite his BishōnenCool Old Guy traits, is still this trope. He has to wear a biohazard suit just to prevent himself from killing everything around him accidentally. When he does take off his helmet, he has areas of rotting around his eyes and temples, as well as several places on his chest and stomach from his disease.
Wolfenstein, especially when he fights or transforms. Unlike most werebeasts, he transforms into a liquid-like state made of blood, fur, teeth and eyes. When he does fight, he turns out to be a Blood Knight with an immense Slasher Smile and I'm a Humanitarian traits Up to 11. It's fairly shocking, especially the first time it's shown against Nitro and even more so against Mortem.
In the first DLC, the Carnival of Carnage is this when you think about it. Mr. Vangorium goes to a planet, and kills everyone on the planet, sparing absolutely no one, then sets up shop. Then it gets scary. He completely supports Masher's psychotic and Serial Rapist tendencies, and Suture's experiments on Aurai, along with using Aurai as a human charger for the Vault Keys he uses on each planet.
While Sirens in the original name have fairly conventional powers, Titans all have a Dangerous Forbidden Technique as their primary abilities. Dion has plasma (meaning his skin and body melt), and Suture has blood (meaning he shoots it form his veins, makes blades, detonates his entire body or forms armor out of it). Rocko seems to avoid this, though that's likely due to lack of screen time.
Grave Lord Arlon's real power, To Name. Basically, this means he can change the name of any object he chooses, altering its function and composition. Doesn't sound so bad right? Well that includes people too. The first two people he used it on were turned into Fire and Hunger respectively, which made them burn down to ashes and crumble into dust respectively. And there's nothing you can do about it to fight it. Unless you're Mockingbird.
Davis Dalmer from the Eddy Tsar's Five Weeks of Hell is rapidly growing to become one. He's a violent sadomasochist with clear sociopathic tendencies. Let's list his actions in order:
Creates human pincushions using massive blades, mostly out of defenseless women.
When Zodd ripped out his piercings in a bar, he proceeded to give him a Glasgow Grin just like him using only his fingertips.
Captures and gives hundreds of piercings to Mary Jane after her fight with Dr. Ivanlove.
Cuts off his own tongue when he was asked for recompensense. He even enjoyed it.
It really says a lot that he appears to be getting more WTF reactions then even Masher did.