This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Hivefled
The file scene. The file scene. This troper was cringing at the just the thought of it.
There are over 2400 Kin. And worse, those are just the ones who lived long enough to sign the Sul. Plus Tsukey; she didn't sign, but is too afraid to go on into death alone and latched onto them.
The Q and A sessions, mainly anything answered by the Grand Highblood and Condesce. They're just so blasť about all the deaths and tortures. What's worse is that they both make a pretty convincing case that as horrible as their relationship is they probably keep each other's total body count down. Just stew on that for a few minutes.
The Condesce cut out the Psiioniic's superfluous organs, cooked them and ate them, making him eat them too.
The Grand Highblood has a skull pile. As in, a pile of troll skulls. Most are probably the Kin's.
Laneen, despite being the child of the Psiioniic, didn't have double horns. The Condesce drilled holes in her skull and implanted them. Worse, there's actually a picture of Laneen in the stocks while the Condesce looms over her with a drill.
The deaths of many of the Kin: Vanate died from drinking the sewage-laced water in the Trap, Keskay was eaten alive, and for extra Squick points, Rasasi was forced to drink from a filled bucket as part of a dare (the dare being if she could drink fast enough to stay alive. She couldn't.) Tsukey was tortured for information and killed by the Grand Highblood (garrotted with her own stocking).
A sidestory reveals that the Condesce and Grand Highblood imprisoned the Sufferer's family where he couldn't see or hear them, but they could hear everything, then raped him while forcing them to listen. It's not necessarily unexpected that they would do that, but it's still nauseating. (Although the fact that this is not unusual for them, and probably isn't even the worst thing they've done, could qualify as this trope in of itself).
Eridan's backstory was written as self-Nightmare Fuel for the similarly Asexual co-author.