This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Inheritance Cycle
The men with no pain.
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.
That may or may not have been a rumor, which could make it worse. But you know what isn't a rumor? The fact that both Selena and Murtagh, and others, can be bound with magic the way they were. 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!?!
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.
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."
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.