This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Shadowrun
Shadowrun's Third Edition Cybertechnology sourcebook is a good source of this, particularly move-by-wire implants and cyberzombies. Both are revisited for Fourth Edition in Augmentation.
The move-by-wire system, like most reaction-enhancing 'ware, is a horrifically invasive implant, but MBW puts the body into a state of constant seizure and works with conscious muscle control to decrease signal latency, effectively giving the user superhumanly fast reflexes. The downsides are if the control unit is damaged, you have no conscious control over your body's movements and users typically develop temporal lobe epilepsy with complications (TLE-X), which persists even after removal of the implant. Symptoms include seizures (uncontrolled now) and mood and personality disorders. The only way to fix it? More invasive brain surgery. Yep, really good trade-off for that edge in combat, chummer!
Cyberzombies are metahumans implanted with more cybernetics than their essence can handle, with magic binding their souls to their now-dead bodies. The soul of the cyberzombie knows that it shouldn't be alive and that knowledge causes them to stop working on a cellular level without a horrific cocktail of obscure magic and medication. Even then, few last longer than a year before cancer and necrosis rots their bodies away and they're almost never even in the same time zone as sanity. A section of Cybertechnology follows the creation of a cyberzombie: the signature character Hatchetman.
On the magical side of things is the Blood Mage Gestalt in Aztlan (SR Mexico). At best, they are sacrificing hundreds if not thousands of people yearly "Aztec"-style to keep their President from parts unknown alive. At worst, it's to speed up the return of the Horrors from Earthdawn (see below) to our world. Usually, though, they just kill people to power-up their spells or to summon spirits into the world comprised of the blood of the sacrificed victims. These spirits would be more than happy to engulf and drown you in that blood, if their master orders it.
Ritual magic is a fridge horror version of this, period. Harlequin's Back implies that ritual magic (blood magic or otherwise) causes spikes to form in the ambient magic of the astral plane. Spikes that the Horrors can use to cross. So regardless of intent, the Blood Mage Gestalt is definitely shaving off time before the Horrors start their comeback tour.
The spell Turn to Goo does Exactly What It Says on the Tin: it turns the subject into an amorphous homogenized mass for the duration of the spell, which is thankfully unconscious. This wouldn't be as big a deal if it turned the target entirely; it doesn't affect clothing, gear, or cyberware implants. A popular tactic is to turn a target into a puddle of snot and then pull out their implants before ending it. A Lot of popular implants are load-bearing like limbs, eyes, and nervous system augmentations.
Bug City. The Chicago sections of Real Cities is probably the most unnerving part.
Lockdown. Later books reveal Deus's semi-understandable motives for creating that hell, but that does everything but justify his actions for turning an entire miniature city into a game of System Shock with brainwashed slaves and Creepy Child cultists with Glowing Eyes of Doom all so he could live in the physical world.
Arguably, what happened to the arcology after Deus was destroyed is just as bad: it became low-income housing. There's no funny plothole, because that means millions of people are stuck there without any hope of advancement, being given the cheapest possible food, water, and clothing, shown only corporate propaganda, with their only chances for money being the most menial labor in the ACHE or medical experiments. And they can't leave. Ever. After all, this is supposed to be a self-sustaining facility, right? Oh, and we almost forgot... not all of Deus's creations were weeded out.
The first metaplot arc in the Shadowrun universe concerned the Universal Brotherhood. The Brotherhood was a beacon of hope in a hopeless world, a charity that offered food, shelter, and medical care to the poor and SINless. Finally, someone's looking out for the little guy! It's too good to be true! It was. The Brotherhood was under the control of insect spirits, using it to gain hosts for more of their kind so they could invade the world.
And to build on it, Harlequin's Back revealed something about the bug spirits: They're the advance scouts for the Horrors, which is a whole different bag of nightmares.
In the real world, they tore down the Kowloon Walled City in the 1990s. In Shadowrun, the refugees from the Chinese Civil War rebuilt it. Now it's home to hundreds of thousands of people who have no way out, paying their rent to the Triads because the regular people don't dare go in. Kowloon itself isn't that nice, but the Walled City is so full of suffering and pain that the Yama Kings have manifested and are slowly grinding away at the souls of the people trapped there. The Universal Brotherhood tried to reach out to the people within, but the Yama Kings are so powerful and twisted that they consumed every insect spirit they can catch.
And it gets better: It's all intentional. A corp is literally leeching all the good luck, and any possibility of a better life, from every resident of the Walled City. Also, the machine that's doing it for them is slowly tearing a hole in the astral plane. The kind of hole the Yama Kings, and Horrors, can come through.
And then there's the Horrors. You see, there are these things from beyond any world that the human mind can understand, and they feed on pain and suffering. And even the weakest among them could take down a dozen men single-handedly. Thankfully, they are incapable of surviving without a great deal of ambient magic, so... oh. Wait. The world's magical potential has only risen since 2012. The last time they showed up, the only way any sentient life survived was burrowing into tightly-sealed chambers of magical earth. And that time, we knew they were coming. It's been suggested that Metahumanity will finally develop the magic and technology to beat them before the upcoming Seventh World, only problem is that won't happen for another 3,000 years.
And the only thing that's keeping them at bay for now? The Dragons. So having no choice but to have someone like Lofwyr have so much power and control as he does over people can be a horrifying thought in of itself.
There's also one more Horror-related nightmare that the world writ large is unaware of. You know the Great Ghost Dance? That event that brought magic back into the world in a big way? It almost started the Horrors' invasion early, too. It was thankfully delayed, but at a cost. Harlequin was Brought Down to Badass, and at least one runner is implied to have sacrificed themselves. And this was merely to buy time.
Cognitive Fragmentation Disorder - the viral form of self-replicating AIs that has made the leap from digital to physical systems. CFD will infect anything more complex than a calculator - commlinks, cyberware, and biological brains, rewriting the host with its own personality. It is 100% infectious on contact, it is incurable by any means magical or technological (indeed, most treatments just make it *worse*), and as the user starts losing control to a completely foreign intelligence in their own mind. These invading personalities vary in intent, but are almost universally hostile to anything that isn't them, and most have no qualms with spreading their infection to make new copies of themselves. It's theorized in-universe that the only reason CFD hasn't ended the world yet is because of it isn't airborne - yet.
As of Lockdown, CFD has gone full on Zombie Apocalypse in Boston with the new Cerberus Strain. What's worse is that these Head Cases have developed abilities beyond simply infecting others; they have hacking powers similar to technomancers, and can use the nanites in their bodies to enhance their physical attributes, keep conscious after they should be knocked out, resist toxins, resist physical damage, and develop a healing factor that can even regenerate from lethal injuries such as severe brain trauma. The worst aspect is that it's confirmed that the host's mind is never truly erased and exists in an And I Must Scream situation while the virus is in control. The bulk of these head cases are feral ragers and shamblers, but there are more intelligent haters, as well as the hidden, who can pass off as non-infected. And of course, those who had the most seamless transition are now possessed either by the intelligence of a dragon, or by Deus himself.
It gets WORSE the Cerberus Strain was created to return the mind back to the body of Eliohann, a lesser dragon whose mind was lost in Crash 2.0 as he is the only dragon with a functioning data jack. Its been implied that the Matrix Ghost Cerberus IS the remnants of Eliohann's mind and a variant of CFD could be used to 'infect' the dragon's body and restore his mind. Unfortunately for everybody the followers of Deus subverted the process and tried to override Cerberus's program in the nanites with Deus. Eliohann's body broke free during the process and took off toward Salem. We still don't know whose REALLY in the mind of the dragon body...