This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Tower of God
Deaths in Tower Of God are scary. The first test in Evankhell's Floor involves the death of two hundred Regulars, and that's just the beginning. Death is commonplace in the Tower, and so are betrayals. People will kill you if they could get the chance to climb higher. Crapsack World indeed.
Not to mention the other off-hand deaths like you get when the Hand of Arlen blows sky-high. There were a lot of tents around there, not just some syspencycles. Or the unknown number of Rankers Urek dusted before that, even. Let alone the two he killed in no time on-screen. Add to that the horrible thought that some of the creatures we've seen killed on and off could have some degree of intelligence even if they're being puppeteered by others... and... *shudders*
The Workshop Battle arc has several disturbing deaths too. One overconfident regular gets his head destroyed by Mad Dog of Yama, and when Koon Ran uses his full might, the collateral deaths are scary (such as one guy having been obliterated except for his arm).
The Devil of The Right Arm arc is full of these.
In the first chapter, the Workshop is revealed to have done countless experiments to make the weapons Regulars use on a daily basis. Human Experiments. It is implied that souls are used to create ignition weapons. The Thirteen Month series, which includes the Black March and Green April mind you, are confirmed to have souls. Let that sink in for a while.
YMMV on this one since the only confirmed case of this was with the Workshop members working with FUG to create the Thorn. It is explicitly mentioned that human experiments are banned by the Workshop in general. And since we don't know how Ignition weapons are made it might be better to give the Workshop the benefit of a doubt.
And now there's Creepy Child Verdi. At first all we saw of her were a few panels of her looking spaced out, holding an octopus plushie. But in chapter 60, the first thing we see of her is her controlling the octopus (Now extremely large) and holding Prince and Miseng, saying that she liked them, will turn them into dolls and make them marry.
There's also Lo Po Bia Ren, the R.E.D. member. Controlling giant fish, exploding in a giant mess of wierd blood, and seems to be certifiably insane. That settles it - all anima are terrifying.
Heck, keep it simple: all Anima are just plain Nightmare inducing if you stop to think about it for three minutes. Even the apparently nice ones. The whole thing screams "Marionette Master" — and the perversion potential is... worrying if you get somebody swimming a little too far into the deep end or who just botches up horribly now and again.
And now it's confirmed that as well as being an Anima, she's an actual Puppet Master. The octopus doll is played for laughs, but Miseng being turned into a bloodthirsty, lifeless doll? Not so much.
Hoaquin, from the Hell Train. His past, present and possible future is the epitome of Nightmare Fuel in the Tower so far, be it because of his ability -and need- to devour the souls of the living, his swordsmanship, his origin or the very sadistic cruelty with which he inflicts pain and suffering to all those below him. All so that he can become White again, the 10th Slayer of FUG and continue his reign of terror from where he left on over 600 years ago.