This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Inheritance Cycle
Murtagh's account of his first meeting with Galbatorix and what convinced him to get the hell out of capital. So Murtagh was summoned to dine with Galbatorix and finds him surprinsgly nice, despite the kings reputation and Murtagh's own experiences with his father the cynical young man starts thinking that perhaps the king's isn't so bad after all. Then in his next meeting Murtagh is confronted by the King after some of the Varden have attacked his soldiers. Galbatorix is in a rage nd orders Murtagh to take a group of soldiers to the site of the attack and punish put any locals who took part in the attack. When Murtagh asks how he is to determine who is guilty and who it not. Galbatorix orders him to raze the town and kill every man, women and child in the place deeming them all guilty. This is the first current account of Galbatorix the readers get and it paints a rather worrying picture about the sanity of the most powerful magician and ruler in the land.
The men with no pain, especially with their giggling - they earned their title of 'The Laughing Dead'. Even the Urgals fear them, particularly since they resemble possessed ghouls from their culture.
To clarify someone on the Empire's side had the brilliant idea to magicially remove the ability to feel pain from a group of soldiers. These Soldiers are not tougher or stronger than normal humans they just keep fighting on with injuires that would normally incapiate a person in crippling agoongy and they are constantly laughing. As one character notes, when you see a man with half his face skinned off, an arrow through his the gut's come at you howling with laughter it tends to shake you.
Selena, Eragon's mother, before her Heel–Face Turn, when she was still known as Galbatorix's assassin "The Black Hand". To test her skill and creativity, her lover Morzan taught her the magic word for "heal" (and nothing else) and then pitted her against some of his best warriors. She healed them of their fear and anger and all the things that made them want to kill her, basically turning them into placid, mindless idiots, then slit their throats. It's pretty hard to accept her Heel–Face Turn after what she did... though as said by Oromis, tales of her exploits have grown twisted, and probably not entirely truthful. But it's never made clear just how much was willing, or what wasn't...
But you know what is clear? The fact that both Selena and Murtagh, and others, can be bound with magic the way they were, doing anything that's required of them. Anything; imagine it. You're forced to do whatever someone says, and your body will do it for you even if you try to resist.
On a related topic, you also have even the weakest magician being able to read anyone's mind at any time without being detected, not to mention Mind Rape. And in Book 4, Galbatorix does just that to Nasuada. He starts out pretty tame, just a few simple tricks (such as manipulating the flow of time). He follows up with an illusion where Nasuada thinks years have passed, she's happily married, and has kids. When this fails, he puts her in a dream where she's being repeatedly killed. Nasuada starts laughing. And later, Galbatorix slowly takes Eragon's mind to pieces. Yes, he gets better, but really! ERAGON, the insanely powerful Dragon-Rider. Imagine what an ordinarily powerful magic-user could do to Muggles like us!?!
Eleva's condition both in its implications and its circumstances. Eragon is asked to bless a baby, with the best of intentions he does so invoking the Ancient language over the child so that she may be shielded from harm. Only it the next book does it come out that because The Ancient Language is a language with gramma and subtext that what Eragon actually said was "May you be a shield from suffering". The poor kid was cursed to be aware of anyone and everyone suffering in the area around her no matter how small or great the circumstances and was compelled to try and and help. If she refused to or was unable to help she suffered pain and distress. Since a babies body couldn't act on the spell's directives she was forcibly aged up both physically and mentally to a point where she could.
Elva herself is fairly unsettling: she looks like a little kid, yet she talks and acts like an old women, is viciously bitter at what has happened to her, she can see all the things in peoples heads that make them suffer emotionally ans is perfectly happy to exploit them ruthlessly. When Eragon manages to alter her curse so that she is do longer compelled to help others but leaving her with the ability to perceive others suffering she is a little too happy about the potential abuses of her power now open much to Eragon's alarm.
The Ra'zac and Lethrblaka, but even more so their worshipers in Dras-Leona. As a degenerate, bloodthirsty cult that worships ancient, horrible monsters, they're actually quite reminiscent of H.P. Lovecraft's towns with dark secrets, and Christopher Paolini may have been inspired partly by Lovecraft. And the High Priest (Priestess?) is severely mutilated (he/she is missing arms, legs, and part of his/her tongue, probably willingly so as self-dismemberment is a regular part of their cult), and possesses incredible psychic powers.
This one deserves a bit more emphasis. These worms? They aren't described by an onlooker to the process. No, they're being described from the point of view of the person who is being eaten by them as a form of torture. Of all the creatures in the book, they're probably the most straight-up revolting and terrifying.
Also, right after we see them being used as a torture instrument, we cut to Eragon, on Doru Arabea, finding some weird-looking worms and having no idea what they are capable of. Good thing he treated them with the same caution anyone would upon confronting something unknown, possibly hostile...
Everything about Vroengard. The place is basically radioactive, seeing as it was annihilated by a Fantastic Nuke (you can replace any mention of 'magic' when the contamination is mentioned with 'radiation' very easily). Burrow grubs, those disgusting carnivorous maggots which Galbatorix uses to torture Nasuada, originated there. It's also populated by giant man-eating snails that move as fast as a running human. What's worse is that they were on Vroengard before said Fantastic Nuke. They survived the equivalent of a nuclear explosion and the resulting fallout.
The fact that any magician with the appropriate knowledge could have the power to command energy on the nuclear level.
The description of the pile of bodies at Yazuac is both horrifying and depressing, considering the true emotion and sentimentality Paolini packs into that one paragraph. No wonder Eragon was so distressed by the sight of it.
"Slaughtered men lay over the women they had tried to protect, mothers still clasped their children, and lovers who had tried to shield each other rested in death's cold embrace. Black arrows stuck out of them all. Neither young nor old had been spared. But worst of all was the barbed spear that rose out of the peak of the pile, impaling the white body of a baby."
Shruikan's situation and the end result. To clarify the book's show that the bond between Dragon and Rider is a thing of absolute intimacy with both souls having fundatmental access to the others deepest thoughts and feelings to the point where they a closer to a single being with two bodies at times. Galbatorix was driven crazy by the loss of his Dragon and tried to recreate the bond with another, Shruikan. The connection between Galbatorix and Shruikan is repeatedly noted in universe to be an abomination and perversion of a real Dragon/Rider bond, forcing Shruikan to serve Galbatorix when he really doesn't want to. Further Galbatorix used magic to make Shruikan grow to the size of an elder dragon, making him a borderline Kajuu, and as a result of this enslavement Shruikan has the mentality of a rabid animal wanting nothing more to kill and kill and never stop.
The assassin who comes after Roran. He keeps insisting he's a friend, then attacking when Roran lets his guard down. He keeps using that tactic long after Roran has stopped falling for it, and keeps saying it until he dies. It's overall rather unsettling.
Carn killing an enemy spellcaster in Inheritance,after being burned to a crisp. His spell draws all the moisture from his opponent, even after said opponent is obviously dead, until the opponent is a pile of dust in the middle of a puddle of water. Roran was quite disgusted by this himself.