This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / The Kingkiller Chronicle
The Denner Resin in general, given that it's shown to be highly addictive and ruin the lives of most users. The creepiest scene, though, is when Denna realizes she's eaten it, and worries that she might become an addict.
Kvothe returns from a frolic in the woods to find his troupe's wagons burning, his family murdered and bloody on the ground. A group of strangers sit at his parents' fire; one of the figures obviously inhuman, with completely black eyes.
The Chandrian. Any scene in which they appear or are mentioned is enough to freak the hell out of most people reading the book. Much of the fear surrounding the Chandrian (for in-universe characters and the readers both) is the fact that we know hardly anything about them. No clear motives, no patterns, not even how many of them there are. Just "Lightning from a clear blue sky". And trying to find out details makes bad things happen.
Kvothe's cold-blooded murder of the fake Edema Ruh clan. His reasons? Totally understandable, but damn. May also count as a Crowning Moment of Awesome.
Sort of the opposite of why the Chandrian are scary, the extermination of the bandits would easily be interpreted at anger over their crimes, making it a pretty understandable heroic action. But his thought process is instead fully explained, and it's clear that he's mostly killing them because they're... making the Ruh look bad, more than anything else. Sin of Pride strikes again, and you wonder if next time the reaction won't be as incidentally deserved.
The Cthaeh: Looking into your future, then leading the conversation in such a way, that your life will result in the most disastrous outcome possible. Not just for you, but for everyone around you. Everything happening right now in the story is happening because of what it said to Kvothe, and the more people he interacts with, the greater it's influence and potential for harm becomes.
Bast's reaction to it could count as well. We've known him for the past book and a half as someone who's rather silly and cheerful (except when it comes to defending Kvothe, but still, an easygoing guy). And when the Cthaeh is mentioned, he FREAKS OUT. Horrifyingly.
The Plum Bob. Just think about someone going around with absolutely no concept of right and wrong, and how much damage they could do when murder seems on par with stealing a pie.
The absolutely terrifying things one can do with malfeasance. Ambrose gets some of Kvothe's blood after Kvothe breaks into Ambrose's rooms. Kvothe is subject to hyperthermia, hypothermia, and random stab wounds, and has no idea who is doing it.
What Kvothe does to the bandits hiding in the Eld when he begins attacking with sympathy.
Kvothe and four other hired mercenaries assault a fortified bandit encampment. The bandits outnumber Kvothe's squad four to one, so when everything goes to hell what does Kvothe do? He gets a corpse and pulls his knife. The bandits get invisible knives stabbed into their kidneys, their eyes, cutting their throats and the tendons in their legs. And they have no idea what's happening or how to stop it. He then turns a tree in the middle of the encampment into a huge lightning rod. The tree explodes, killing almost a dozen of the bandits and all but destroying the camp.
Sympathy magic in general is this once it's clear that the usual superhero limitations on that kind of thing don't apply and it can be as easily applied to people as anything else energy and cost-wise. It's a good thing none of the characters have seen all the voodoo movies and novels that the average audience member has, otherwise the setting would sink into Conan-style dueling sorcerer warlords in about five minutes. For that matter, it has done exactly that at multiple points in the past.
And after you read all of that, go back to the Plum Bob. What it happened to Kvothe needs for the Plum Bob to be circulating in the Academy. A place full of people capable of using sympathy. Now let that sink in.
Onomancy doesn't become one only because it's extremely harder to use, let alone master, but it's far scarier. Studying it is enough to make people lose their mind. And that happens, quite frequently, to the point the Academy has a quite large asylum built in for them. However, once you mastered something's name, you can make it do anything, without sympathy's drawbacks and limitations. The first time Kvothe uses it, he calls the wind to hit Ambrose and compares it to the hand of god hitting him. And you can know people's names...
When you think about it, Felurian is a serial rapist/murderer. She forces people to have sex with her against their will by using her innate magic, and continues until they go insane or die. Kvothe's flashback to his attempted rape on the streets of Tarbean is what lets him break her control, which seems to hint that Rothfuss isn't blind to this fact.