The "Fast Times At Achewood High" arc (starting here) begins normally enough, but then it veers headlong into some pretty unnerving territory. To make this worse, this is coming off the heels of a pretty bittersweet arc with Philippe and his family. Thanks a fucking lot Onstad
Dominic Deegan - the last panel of this strip makes it clear that that guy Stunt left for dead is totally being consumed alive and conscious by the slimes. Just look into his eyes in that last panel...
Hedone High: "The Smote's Lullaby" is a fan song for an A Uish animation. The basic story is that it's the singer warning their child about "The Smote" (Izm). They tell them various things that The Smote will do to them, including sewing their mouth shut, blinding them, and then killing them. It gets even worse when you apply some of the lyrics. "Please be good, my dear sweet child, or The Smote will get you too." Why is this scary? This implies the singer has been/knows someone who has been killed already. Now think of the character in Hedone High that cares for children, was killed, and knew The Smote personally...
Grey from Inhuman His occasional backstory flashbacks occasionally show his body being torn apart/altered in various ways. That and the fact that whenever someone gets shot with the special Rulerist ammo, it's always in the face, and part of their head basically goes all 'splodey depending on where the bullet enters the face. It's happened twice. So far. Oh, and let's not forget Grey tearing that one guys organs out with a kitchen knife with a bit of a gut hook in the blade, and the one whose throat he slashed open, and the one he blasted with static electricity that he had built up over the day, the fact that Grey's a 'certified schizophrenic' (in his own words), the fact that his shadow LITERALLY talks to him (He's a telepath, interestingly enough. Other people see it too.) and the freaking headworms that sometimes sprout from various parts of his body and start trying to eat him alive. In fact, anyone who reads that comic and doesn't agree that it's some form of Nightmare Fuel should get their head checked. And perhaps the artist should too.
It IS very graphic and a good read.
The second flashback of Soshiko and Kyo's parents being murdered. Especially when it turns out that it was done by Hekshanians.
The premise for the story arc "Suffer" was becoming disturbing enough... then Dripshows up.
The arc, "What's Pissing Off Dalton," is terrifying. People are trapped underground after an earthquake, in an inclosed space with a psychopath off his meds who snaps at the drop of a hat, brutally beating people to death for the most minor of infractions...
Kaspall has the Veritarc. The Veritarc is an entity born out of a children's scare story about lying, and we all know how terrifying those can be. He appears as a man in robes, carrying a walking stick, with his head covered with some manner of sack. The Veritarc comes for those who make a promise and break it... any promise, broken for any reason whatsoever. The Veritarc sends his children after you, living shadows that can appear from any dark place as though it were a door, and they collect you and send you to the Veritarc's home, a cold hall at the edge of the world. You can either sit there and wait for him, or run and make him chase you, but it's all the same, The Veritarc will slowly, relentlessly follow you, it's walking stick tapping in pace with every step he takes, until you can run no longer, and then he will catch you, and then... well, the next morning, they find you dead in your bed, with your little finger cut off.
The fate of the four jerk jocks in The Wotchtries to be Karmic Transformation, but only manages to be utterly disturbing with the fact that 1) they're STUCK and 2) their memories of their former selves are erased, leading to a disturbing case of Not Himself. And Jo? It's the WORST. They were going for funny, it ends up even more disturbing than the above. Also, what happened to Scott, his girlfriend and Ivan. Damn YOU, Miranda.
Ming Mei's story as well, with a huge dose of Ass Pull to boot. But really, let's say that the whole Consequences arc is HONF, especially because we know the leading girl has done a LOT OF DAMAGE, yet the aforementioned consequences NEVER COME.
Mindmistress - specifically, what MM does to Anansi Webb. For those who don't get it, she's not really turning Anansi into a spider - but making her think she is works just as well...
Some of the things seen in Nature of Nature's Art are... disturbing (the fact that the characters are animals may or may not make it worse). For starters, the first arc, 10%+, involves sapient animals being stripped of their human-level intelligence and left as mindless base animals. Now think about the effects that would have on a human being...
Meanwhile, Secretary has the incomplete Malice Style, which can have such wonderful effects as having your body fall apart with pieces of corn coming out and punching the bonesout of your arm. And the complete version of it... well, there's something to be said about ripping open a female jerboa's innards... which turn out to be inner demons in the form of jerboa fetuses... and to top it all off, as SV is dying, he has a hallucination of himself melting away into a skeleton. Secretary is just plain charming, isn't it?
Mieville. Oh dear God. Played for laughs in the comic directly after that.
Schlock Mercenary's "Schlocktoberfest" storylines ranged from the merely macabre to the downright terrifying. This editor is still trying to repress the 2007 storyline (involving, among other things, a grotesque, animated headless corpse, and nanobots leaping from said corpse after turning into miniature lizardlike monsters bent on destruction).
The one from 2001 involving the crew fighting a bunch of Alien style creatures would have been scary enough, but having it from the alien children's point of view somehow made it even scarier and more depressing. The way Schlock finishes them all off is mild in comparison.
Normally, The Zombie Hunters doesn't really scare me that much. At best, I get disturbed by a few things here and there. But the scariest thing I've seen in the strip actually wasn't zombie related. Look here. The faces in the first two panels. Those freak me out whenever I look at them. Normally, the artwork is very lovely to look at, but something is a bit...off with these guys' faces, don't you think?
Vampire Phantasm & Vampire Phantasm Excrucio. VP starts off with Orlock murdering the Jack's wife and baby daughter by ripping them to pieces, turning Jack into a vampire, and spending the next century torturing him into insanity. Excrucio is worse.
The deaths of Sean, Alec, Mao, and Evan in Sonichu are horrifying; Alec is given the chair, Evan is genitally mutilated by drills, Sean is put on the firing range, and finally Mao has his limbs telekinetically bent and snapped, before his heart is exploded. *shiver*
And it gets worse when you consider why they're being killed. Both in-universe and out, the four of them worked together on a parody of Sonichu. And that was it. Oh, and Evan had a character stolen from him and used in Sonichu and demanded the artist stop drawing the character and give it back. That's it. Disproportionate Retribution doesn't even begin to cover it.
The alt-text that goes with thisxkcd strip, particularly because we're on that path:
The universe is probably littered with the one-planet graves of cultures which made the sensible economic decision that there's no good reason to go into space—each discovered, studied, and remembered by the ones who made the irrational decision.
U13 Kakarotto...just see this page◊ and Chapter 27... Made even more horrifying by the single fact that, had the Goku we know and love not hit his head as a child when his ship landed on earth, that's what Goku would be today... Oh, it gets worse. Turns out Kakarotto and Krillin were good friends, and for one panel, we see Kakarotto being as innocent as his U18 counterpart.
The Kaioshin's rather direct way of dealing with upcoming dangers, like killing Frieza and Cooler when they were children and Broly when he was an infant, in the Universe 1/10 Special was noted to be too violent by fans.