This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / A Hollow in Equestria
Chapter 16 when Ulquiorra explains how the dragon would've killed the mane six without his intervention. That in itself isn't terrifying since he was there to help. The Fridge Horror kicks in when you realize that the whole dragon episode would've still happened even if he wasn't there to intervene, meaning they WERE going to be killed.
Chapter 17 is chock full of unapologetic Nightmare Fuel when Ulquiorra's true nature is revealed to the mane six. Applejack's realization that a murderous, soul-devourering beast had been in her house and around her family. Pinkie promptly points out that he could've devoured the souls of everyone in Ponyville if he wanted to. Ulquiorra does nothing more than confirm that they're correct, almost as if he was proud of them figuring it out.
Chapter 18 gives us Luna's tale of being possessed by the entity of Nightmare Moon, rendering her a prisoner in her own body, and forced to watch as her form was used in the butchering and devouring of 17 innocent foals. More than a thousand years later and she still isn't over how the last thing they saw was her face before their souls were ripped out of their bodies.
Chapter 22 is Nightmare Fuel from beginning to end. But while the beginning is horrifying, the middle of the story explicitly spells out that while Ulquiorra was going about slaughtering every changeling in Ponyville, the carnage even occurred in the schoolhouse in front of every foal assembled, who witnessed him killing several of their classmates in truly bloody fashion, before the spell broke and it was revealed that they were changelings.
Chapter 25 is Nightmare Fuel from Celestia's point of view. Since chapter five it's been believed that Ulquiorra's release was sealed away and inaccessible. Then she finds out that he's been lying to her the entire time, and could utilize his resurrection at anytime she wanted. Making it all the worse is the release itself occurring overhead and the massive wave of black/green energy completely blotting out the sun from her view.
Chapter 25 gets even worse near the end when they all believe Celestia was actually killed in front of them.
Chapter 28.5 when Ulquiorra theorizes that the mane six are under attack by some unidentified threat using a systematic approach to trying to kill them. The entire chapter is more or less about lining up why he believes this, and laying out the questions that they have no answers for. It gets so bad that even Ulquiorra, the one without an ounce of fear in his entire body, comments that the phrase "scared shitless" is highly appropriate.
Chapter 42 gives us Zecora's mention of roho mlaji after hearing Ulquiorra explain what Hollows are. She claims his description sounds very familiar to legends from her own homeland, leaving Ulquiorra to speculate on whether or not other Hollows have found their way to Equestria.
Late chapter 43 and early chapter 44. A good portion of Ponyville is partying at Sweet Apple Acres, only for the get together to be crashed by a bloodied and mutilated Pipsqueak announcing that Ponyville's under attack. That's certainly a party that no one is ever going to forget.
Chapter 45 gives mentions Sweetie Belle, Apple Bloom, Scootaloo, Silver Spoon, and Diamond Tiara being attacked by a timberwolf in the Everfree Forest. According to the exchange between the fillies, the only reason they escaped alive was because the timberwolf tripped over Diamond Tiara when she fell down while running away.
Chapter 58 and the last line about the Element of Loyalty fading to black.
Ulquiorra's theory that a virus is responsible for everything going on. Imagine a virus that can drastically alter your own memories and experience, and you have no idea if it's airborne, waterborne, spread through touch, or just how contagious it is.
Chapter 59 gives the idea of what Ulquiorra might do if he knew about the Element of Loyalty not working, and being tied to rainbow's life
Chapter 60 Rainbow Dash's first reaction to being asked to step forward after confessing she did something bad is, "I don't wanna get hit." implying her mother was physically abusive if ". . .like the time dad made me tell mom I broke her vase?" is to be a hint at that. If you don't believe her when she says it was because she was being greedy.
If you stop and think about it, chapters 57 through 60 are true nightmare fuel material. Ulquiorra contemplates how it would be impossible for anyone to know for certain whether or not their own memories have been altered, with his own pondering over whether or not he's been affected as well. The concept itself is so terrifying, even Ulquiorra can understand how one could be afraid of it.
Chapter 61, about 90% of it at least.
Chapter 66 is equal parts Nightmare Fuel and Fridge Horror, and might even be worse than what happened to Applejack back in chapter 62. Back in 58, Luna pretty much established herself as the Mama Bear type to Rainbow Dash, vowing vengeance on whoever has hurt her. Fast forward eight chapters and we now have her sitting in the throne room, alone, surrounded by blood and broken glass from when Rainbow Dash came crashing through a window, anxiously waiting for Ulquiorra to get back to Canterlot in order to brief him on what's taken place, and all the while she doesn't know whether or not her surrogate daughter has died from her injuries.
Chapter 67 doesn't go into explicit detail about what Rainbow Dash went through at the hospital, but what it does mention suggests it was quite bad, including being locked in a closet all night long because she didn't like how the doctors were treating her.
Chapter 67 actually gets worse. If Ulquiorra hadn't been present to call Thrush out on the spell put on Rainbow Dash's wings, would Celestia have simply let the so-called doctor take her back to the hospital unopposed?
Chapter 67 supplemental suggests that Doctor Thrush had Rainbow Dash drugged in order to discredit whatever claim she might make if word ever got out about what he does to patients in the hospital.