Soul Eater/Nightmare Fuel

As expected of a series that takes place in a town called Death City, Soul Eater certainly has its fair share of terrifying moments.

Every single Slasher Smile. Every. Single. One. And there are a lot. Often overlaps with Nightmare Face.
The effect of Arachne's insanity: "There are spiders... Tearing at... The inside of my..."
Just the thought of what the FUCK happened to Crona and Ragnarok to get Ragnarok melted with the black blood, and then replace ALL of Crona's original blood with that black blood. Not only that, but what about the effects? Because of the Black Blood, Crona would be literally 'cold-blooded'. He/She wouldn't give off that same human warmth that most people would. It would basically make Crona inhuman. It's no wonder Spirit was so pissed at Medusa for what she did.
The Moon! Oh dear God, the MOON! And dear God, it's even worse up close. It's looking at them. And the Sun! Granted, it's not as bad as the Moon, but that grin.
Here's one more reason to be afraid of the Moon. The KISHIN is LIVING ON IT!!
The Ghost Ship. Not to mention what it must be like being stuck on it.
Earth had been depicted as a weird hodgepodge of time and places. But after being defeated by the good guys, Medusa, in the form of a snake flees to a perfectly normal suburban neighborhood, indistinguishable to the Real World. She takes over the body of a little girl who was with her mother by crawling down her throat. The mother and father know something's wrong with their little girl, but they don't know what. And then she disappears, and the scene shifts to signs of the little girl missing. And those signs are old, so we know she's been missing for a long time.
- And Medusa speaks in such a Creepy Monotone when she's trying to pass herself off as the little girl to the girl's parents!
The Clown is insanity incarnate. And its mismatched eyes and stare will haunt you.
In the manga Crona's Magnificent Bastard mother Medusa forced him/her to KILL A RABBIT IN ONE FLASHBACK. Back to the present, he/she's leaning over Maka, holding Ragnarok over his/her head, his/her scariest face yet on, Maka's head replaced by that of a rabbit.
Additionally, the early scenes of the Demon God Asura leave quite an impression.
- A mere hallucination of Asura literally rips the faces off of Free and Eruka with its teeth and then just disappears. Then later his actual body emerges, slowly, painfully, creeping across the floor towards the protagonists in a way that is completely inhuman. Oh yeah, and this is after Shinigami tore off his skin while he was still alive and used it as a bag to contain him in!
- Plus the awful silence just before he's released, when all you can hear are the chains clanking...
- Then there's his actual face, where there are eyes within his eyes. Looks rather cool, but jeesh.
- Just the sheer Mind Rape that Asura's madness can cause is the stuff of nightmares. There's no way to know when it'll hit you, you can't stop it, it infects you and destroys your personality until there is nothing left, making you a danger to those around you and sometimes driving you to suicide. Something about a complete lack of self-control is truly terrifying. The music in those scenes, namely "Victor", does not make things better.
Tezca Tlipoca, the weapon of the South America Death Scythe, a monkey named Enrique. You'd think he'd be the meister as a human, but you're almost grateful he isn't when you consider he fact that he's a guy wearing a bear mask (reminiscent of Hyde and Closer) wielding whatever a goddamn monkey would transform into in battle.
No 'love' for the Book of Eibon? The thing has teeth, is pulled out of nowhere by Noah, and Kid - who up until this arc has not been fazed by anything very much (asymmetry excluded) - is screaming as he gets dragged into it.
And then there's the fight between Medusa and Stein and Spirit. Or, more specifically for this entry, the way Stein acts during the fight. Stein's shrieking and lashing out with Death Scythe is both awesome and horrible, and the grinning doesn't help.
Some of Soul Eater's music is a mix between Nightmare Fuel and Paranoia Fuel. "Apparition" and "Like a Radio" in particular come close to stealing your sanity. Oh, and comparing "so scandalous" from the first OST to "Soul Eater - Reprise" from the second makes you want to beg Soul to please please please stop using the Black Blood, now.
Giriko's actions towards Maka are extremely disturbing, as he makes it very obvious he intends to rape and kill her. Oh, and we get a handy reminder/guess from Giriko she's 14. Great.
The manga has the Clown chapters where Maka is under a hallucination which starts out as a harmless-seeming flashback, filling in a couple of bits about her past. And then everyone falls down dead. Amidst the other Body Horror and Madness tropes, my worst/best bit of nightmare fuel in this series is seeing a little Maka trying to get her daddy to wake up.
High Octane Nightmare Fuel, thy name is Kishin. When he wakes up, we get to see the lovely sequence of him putting his skin back on on from the inside. Before he actually puts some clothes on, the whole thing can just be summed up as Uncanny Valley to the extreme. Except those weren't clothes... those were make-shift coverings made out of his own skin..
Chapter 22: Medusa's armless torso crawling up onto Stein's back and attempting to bite his neck! Made even creepier when she whispers "I love you~" before he stabs her through the face with Death Scythe. Which we see in a nice big panel. She is still grinning with the blade sticking out of her skull. The anime doesn't show this. If anything, Okubo's simpler style early on only makes what Stein does to Medusa all the more horrifying. Ditto with Crona's mad faces and the 'rabbit' mentioned above.
On the other hand, when Okubo does decide to depict bloody injury, we get stuff like Mosquito beating up Kid, leaving a trail of blood from his missing arm as he throws the boy across the floor. Ow. Oh, and Patti's still in the hand which is lying "all the way over there". Mister Okubo then goes to town with Mifune and Black Star...
The Flying Dutchman getting brutalized by Crona. When he rows away (That's right, he lived!) from the destroyed Nidhogg, his face is laying on the floor in two halves, so you get to see his TONGUE coming out of the top of what's left.
How about Medusa's ability to put snakes in your body? When she told Eruka Frog that she had an indefinite number of them inside her, and Medusa would always find her no matter where she ran, and the fact that at any moment, those snakes could tear Eruka apart from the inside out...
Death the Kid becoming an Omnicidal Maniac in the manga. Sure, he gets better thanks to Black Star. But, still, the very fact that he was perfectly willing to destroy everything (including his own father and his own weapons/partners) just to achieve perfect symmetry through nothingness is nothing short of terrifying. "My skin is crawling...."
Justin Law in chapter 86. The madness version of his 'blade of faith' speech from his debut is also a nice touch and suitably horrible. Anything Justin after he starts suffering from madness can be nightmare-inducing.
Chapter 87. EVERYTHING in chapter 87! This is the first page.
- This is one point that needs to be made on it's own. Those spheres we saw? People trapped in those spheres dissolve and become solid madness! And Crona did that to an entire city.
- Even the title of that chapter is fucking creepy. "Just A Simple Story About Killing People."
Not as bad as the other examples on the page, but creepy nonetheless: The fourth ending to the anime, as well as having some apocalyptic opening images, has a long pan of all the secondary characters lying dead among wreckage and decay. Combined with the much darker tone of the music, it makes for an intense ninety seconds.
While we all know it will (eventually) turn out okay, the scene with the secondary characters is rather similar to the one following Asura's last attack on Death. The explosion leaves the onlookers lying unconscious in the rubble, and Shinigami in pieces, with Spirit having been thrown to the ground elsewhere.
All of the new clowns in 91, especially the White Bunny (in the link directly above). Because one clown wasn't enough.
The fact that, in order to put Ragnarok into Crona's body, Medusa literally had to melt him down like he was an inanimate piece of metal, then mixed him with the black blood and injected him into Crona (who was drained of all his/her own blood). And this while he was apparently a child. Exactly how terrifying and painful must it have been to go through all of that? It's surprising Ragnarok is just a Jerkass and not a mindless, bloodthirsty wretch.
Professor Stein goes completely insane as a result of Medusa's plans. He got better, but still the entire collection of scenes showing his descent into madness is creepy.
- Pretty much anytime anyone in the cast undergoes Sanity Slippage is this. Which is often.