If we're talking about Yami Marik/Malik, we can't really leave out him scraping the skin off of his father's back while the victim screamed in pain, can we?
A number of the card images can be this, especially cards that deal with Dark-attribute or Zombie-type monsters.
Zorc Necrophades. He is large, has fangs, horns and a freaking dragon on his CROTCH.
Correction: The Dragon IS HIS CROTCH!!
Yu-Gi-Oh! (Toei Anime), Yu-Gi-Oh! Duel Monsters and the Manga
Several of the Shadow Games from the Original Manga and the Toei Anime are incredibly dangerous. and many of them are from the main heroes Super-Powered Evil Side, no less. One of the mildest examples of the Penalty Games is SETTING SOMEONE ON FIRE!
Kanekura's Penalty Game is also disturbing, as Ammit towers over him and the shock gives him a heart attack. Neither Ammit itself or Kanekura's shocked face is decent to look at, to say at least...
The chapter when Jounouchi had been forced back into his evil gang, but when he rebelled, they took him to a warehouse where they TORTURED HIM, by beating him and electrocuting him with a taser.
Also, in Chapter 5, when Anzu gets knocked out with chloroform...and it's implied that the guy who knocked her out wants to rape her. Creepy enough...but then, we never get to see what Yami himself does to her, do we? The chapter ends with him standing next to her unconscious body. We have NO IDEA what he could have done to her.
Imori and his Soul-eating Jar in Chapters 46 and 47 of the manga (and the Toei anime). In the manga Imori states that it takes the Jar about 3 months to fully consume a victim soul, implying that you spend 3 months being eaten little by little .... brrr.
The scene of Pegasus receiving the Millennium Eye. In the manga, the scene itself is more ambiguous, Shadi's men merely approach Pegasus with the Eye and what seems to be a knife, and the next thing we see is Pegasus' silhouette and his screams. The anime is much more blatant with Shadi pushing the artifact into Pegasus' eye socket whose face obviously shows pain and then hear his scream. The anime even adds a scene of him trying to get back on his knees, groaning, while holding the left part of his face. Then there's the scene with Dark Bakura taking his Eye out, licking the blood off it.note Manga only, the anime only shows Dark Bakura licking a bloodless Millennium Eye, which was removed from the dub entirely.
The Millennium Items themselves, thanks to their evil intelligence and their possession of an independent mind to a degree. When Shadi puts on the Millennium Ring on a graverobber, it stabs him in the chest and burns his body to the bone because it deemed him unworthy. Pegasus' reaction at the scene speaks for itself.
Shadi: The Millennium Items' ownership is for those whose soul is worthy... Therefore the souls of those who don't deserve them will be burned to death...
The creation of the Millennium Items. Who would want to wear something made of gold and the melted remains of 99 massacred villagers?
Both him and the Millennium Ring are terrifying. Just think about it. You're a shy, quiet, good kid. Then one day, your Adventurer Archaeologist father gives you a shiny little trinket from ancient Egypt, and suddenly, everything changes. You find yourself with strange gaps in your memory and people around you start going into comas for no apparent reason. And most of the time, these victims are your friends, who you were just playing a friendly tabletop RPG with the day before. Then you finally make a new friend with a similar pendant, and then you start hearing a voice in your head. And it wants to skip the comas this time and outright kill your new friends. Oh yeah, and that voice also turns out to either be the vengeful spirit of an ancient tomb robber, an Eldritch Abomination, or some twisted combination of the two. It can take over your body at will, flawlessly imitate your voice and behavior, and do all sorts of horrible things and leave you to suffer the consequences. And no matter what you try to do about it, that accursed pendant of yours just Won't. Go. Away. This thing has you at its mercy, and there is absolutely nothing you can do to stop it.
Don't forget he is probably a masochist, who will willingly harm himself leaving his host wondering what the hell "happened to his arm." Not to mention in the Egyptian season he thieves the pharaoh's sarcophagus and drags it around behind his horse as a bargaining tool not to mention his monster host is impervious to the sealing powers of the millennium items. NOT TO MENTION he's still as evil and wicked when the monster is temporarily removed from him.
Yami Marik is just as frightening. And laughs just as much. Actually, Yami Marik is probably the highest source of horror in the original series, with Zorc Necrophades being the only other more terrifying entity than him.
All the shit he does with his tongue is either seriously scary, or serious Nightmare Retardant, depending on your point of view.
Don't forget he was created by the hatred and pain Marik had to go through as a CHILD when he was forced into the tomb keepers ritual by having the sacred script KNIFED into his back Sure, the dub "softened that blow" by saying it was tattooed but STILL!
No, it does NOT soften the blow. To achieve that level of detail in a tattoo without the aid of modern needles, it's most likely that Marik's was inflicted using a method that the Inuit people used; taking a needle and thread, dipping it in ink and sliding it through under the skin like you're sewing. It leaves nice clean lines and it's reasonably hygienic, but it hurts so much. To prevent the ink from fading you need to get it quite deep under the epidermis. In amongst all the nerves. Seeing the level of detail in the thing, it's a safe bet that it would have taken goddamn days to do it. Most likely with a handmade needle, much thicker than the one in your sewing kit, with rough jute thread to pick up the ink, and the ink itself would probably be some horrible concoction. Sandpaper string. Covered in caustic ink. In the soft skin on your back. For days. Don't you love it when the dub mackeres the situation into something worse?
Another creepy thing with Dark Marik is when a semi-transparent part of his face stretches to the side, usually when Marik is particularly angry or about to do something exceptionally evil. I'm not sure what it's supposed to mean but it's damn creepy.
It's possible this is showing Dark Marik's personality fragmenting further under stress, as Dark Marik himself isn't a fully-formed personality when it took over Marik's body. In the Japanese Manga/Anime, Dark Marik gradually devolves from simply hateful to a slavering animal wanting to hurt everyone he can, however he can. Dark Marik was born from Marik's displaced rage and pain; if Dark Marik's original motivation was "Kill and hurt those who hurt us!", without Marik to moderate it, the motivation gradually deteriorated to "Kill and hurt everyone who gets in my way!" and then finally "KILL HURT KILL HURT".
In the same episode, there was the Dark Necrofear. Even in the dub, that thing was creepy as hell.
And that's saying nothing noise it makes.
In the Japanese version, when she dies, the viewer is treated to a lovely shot of Dark Necrofear's eyes burning out of her head. This was, understandably, cut out of the dub.
Despite the Dub having most deaths be replaced with the Shadow Realm, the idea is freaky. Basically we have what could be consider Yu-Gi-Oh's version of Hell, a place of darkness, pain, and agony where monsters will feast on your body and soul as you slowly disappear into oblivion. In some way, the Dub may have unintentionally created a Fate Worse than Death.
Yami warns Yugi during their duel with Pegasus that his soul would be shredded if he stayed in the Shadow Realm too long.
Pegasus's Toon cards. What happens when the wacky, colorful, silly cartoon characters turn their antics on you? You get a bug-eyed, cackling Blue-Eyes with a mouth full of exaggerated fangs, or a big red Ryu-Ran who laughs as it inhales to blast you to ash with nostril flames. They look like classic American animation Toons, but they are Toons in a card game based around ancient shadow magic and interdimensional monsters, and they are terrifying! Even the non-Toons Pegasus uses are creepy, like Bikuribox, a Jack-in-the-Box who pops out, reaches into its mouth to pull out a giant gleaming scythe, then launches forward on its spring with an Evil Laugh to slice you into ribbons.
And let's not forget how Pegasus creates his Toons - by sending them into Toon World and sealing them inside, if they want to or not. He's essentially conducting Mind Rape on the original monster to turn it into a Psychopathic Manchild of itself. And let's not even get into the idea that Duel Monsters are supposed to be the incarnate souls of humans. Just think about what the Blue-Eyes Toon Dragon means in terms of Kisara...and does Pegasus realize this is what he's doing? The man does seem to like capturing souls...
Right after Bandit Keith (known as Keith Howard in the manga) loses to Jonouchi in the Duelist Kingdom, Keith decided to confront Pegasus in the hall. He held out a knife and demanded that Pegasus give him the prize money. Pegasus' guard prepared to take out a gun, but Pegasus insisted there was no need for a weapon. Pegasus said that he was aware Keith had cheated against Jonouchi and that he intended to punish him. Pegasus deemed Keith to have lost his Duelist's mind when they fought in America and inflicted the "Hand and Gun" Penalty Game on him. Keith's hand was then slowly turned into a gun, which he was FORCED to use to play Russian roulette with, killing himself.
This was changed in the anime, in which he was thrown out of the castle and into the lake hundreds of feet below.
Slifer the Sky Dragon/Sky Dragon of Osiris appeared to be doing its best to invoke this on Yami Yugi of all people when Yami Yugi had to face it, and it was damn well working. He even says that he's frozen in actual fear. The best example is in the manga, even in a cage, protected from the God card, Yami Yugi was practically crapping himself. And then the cage disappears...and Slifer wastes no time in lowering its head so that it's mere inches away from Yami Yugi and eyeballing him with a snarl.
The Doma/Doom/"Waking the Dragons" arc. The whole soul-stealing thing was bad, but considering how we had Yami using the evil "Seal of Orichalcos" card, and going all evil, only to loose his duel, but Yugi took his place so he wouldn't loose his soul, then the duel against Yugi where he used said evil card... not to mention the revelation of who the Orichalchos Knights were behind their helmets... gah that was a really dark season!
Kuribabylon, a larger Kuriboh with two fangs and a horn. Normally it's just as cute as the original Kuriboh, but when Yami Yugi corrupts it with the Orichalcos card, it's fur changes to dark blue, its eyes glow red with a malevolent glare, and its two fangs become a big wide smile of long sharp teeth. *shivers* That's one scary cottonball you've got there, Pharaoh.
Yami is dueling Weevil, who tears up a card saying that it's the Seal of Orichalcos that Yugi is trapped in. Yami goes berserk and uses the whole "monsters are real" aspect of the Seal to beat Weevil to a pulp with a spell card that gives his monster almost limitless attacks. Tea freaks out for good reason.
Guardian Dreadscythe, a darker zombified version of Guardian Eatos wearing a mask. It's big, intimidating, almost impossible to defeat, and it by the look in its eye it likely takes pleasure in destroying its enemies. It beheaded a dragon!
Dreadscythe is literally implacable, it cannot leave the field if you draw enough cards. It will just keep hacking and slashing... and then there is Soul Hunting, its trap card, which works against cards that switch it to defense mode, the only real way to stop it. It is the Grim Reaper, and it now swipes away any defense mode monsters you have, leading to most likely a direct attack. By a big, monstrous thing wielding a huge fucking sickle.
In the manga, Japanese anime, and English dub, at the start of the Memory World arc, Yugi's grandpa gives us a flashback of when he took the Millennium Puzzle out of the Pharaoh's tomb. But in every single version, the puzzle is the only thing that's in the burial chamber of the tomb. The Pharaoh's body isn't there! Maybe sealing away that evil magic came with the price of destroying the Pharaoh's body. And if that's the case.... One of the beliefs of ancient Egyptians was that the body needed to be intact to allow a spirit to enter the afterlife, so if something happened to the Pharaoh's body he shouldn't have been able to enter the afterlife no matter what the outcome of his ceremonial duel with Yugi. He should have been trapped forever between life and death, a spirit never at rest.
It turns into Nightmare Retardant when one thinks about it: The ancient Egyptians most likely buried Atem's body somewhere else.
Chapter 21 of the manga, we have Kujirada's digital pet who, apart from looking absolutely disturbing and scary, eats other pets!!
Then there's episode 7 of season 0, the anime version of that chapter. Basically, Kujirada appears to be the bad guy... until the real Big Bad of that episode reveals himself in the form of a creepy, glasses-wearing little kid known as Haiyama, who until then was considered the victim of Kujirada's bullying. Turns out Kujirada is the victim and Haiyama's the one who bullied him senseless with a friggin whip, and it's implied he has a long history of doing this to big, tough-looking guys to make them do his bidding. Just imagine what would have happened had the Creepy Child not been unmasked... probably one of the few instances in which the anime was darker than the manga
The duel against Pandora (Arkana) during Battle City. Yeah, most of us know that in the Japanese anime, it featured buzzsaws that would cut the loser's feet off. In both versions of the anime, however, Yugi manages to save Pandora before the thing can touch him. He has no such luck in the original manga, where one can actually see the buzzsaw draw blood from what's probably one of his legs' major arteries before Yugi saves him. Even worse? Right after Yugi leaves, Marik looks into Pandora's memories and stirs up any and all suicidal thought's he's had before, meaning that the moment he wakes up, he'll go and kill himself. Keep in mind, this is supposed to be the "good" half of Marik.
The Ventriloquist of the Dead's Penalty Game. Trapped for the rest of the life in an illusion to be tortured by a very disturbing-looking, Chuckyesque puppet version of himself. Shudder.
In the Yu-Gi-Oh! manga, Marik hypnotises Anzu and forces her to take a pill, presumably a Cyanide Pill, between her teeth. If Yugi does not duel Jonouchi, Marik will force her to swallow it. (In the anime, a giant block of concrete was suspended above her head.)
Another example from the Battle City arc, the fate of Seeker, the first Rare Hunter (and Exodia-user) that was defeated by Atem, especially in the dub. Just picturing what a then-faceless villain was capable by witnessing a fully-grown, hyper-confident duelist reduced to screaming for forgiveness in quite visible terror was unnerving enough, but seeing the poor man's eyes, bulging with veins and shaking with fear until the pupil slowly fades away into lifeless Blank White Eyes, with the subsequent involuntary breakdance/seizure thing that Marik forces his unwitting, zombie-like puppet to perform was extremely unnerving.
There's also how Marik possesses him in the manga which makes it even more disturbing to view. While the eye symbol appears over his ahead in the anime, in the manga his forehead actually transforms and swells into the symbol's shape, with him screaming in agony the entire time as it happens until he's taken over.
In the duel with the Paradox Brothers, Yugi uses the Mystic Box on a spider-like monster called Jirai Gumo. When it opens, we get to see the lovely picture of an already creepy spider with swords sticking through it.
Ms. Chono's true face, coupled with her pretty one cracking apart and falling off.
Episode 4 of the Toei anime has perhaps the most horrific scene in the entire franchise. Yugi battles a thug obsessed with watches who stole Honda's—the Shadow Game has them trying to recover it from a periodic spring, before a giant pendulum takes their hand. When the thug tries to cheat, the pendulum automatically swipes across his hand—and instead of blood, he sees gears and sprockets in the gash, and lets out a HORRIBLE scream as his glasses fall off and reveal clock hands in his eyes.
The 4Kids dub added some Nightmare Fuel before Yugi's battle with Pegasus, where his grandfather pleads with him to stop Pegasus, for the world's sake. If he had this much power with one Millennium Item, imagine what he could do with two. The Japanese version had him tell Yugi that he was in pain and to rescue him quickly.
Kaiba's vision of Mokuba being trapped inside the rotting Blue-Eyes Ultimate Dragon, then seeing himself melting.
Tenma Yakou has an Eye Scream moment in the beginning of the series, after discovering the duel table with Pegasus' blood splattered over it and Crocketts telling him that Yugi had won the duel. His eye then melts out in a surreal scene. Since then, he would usually have a case of Mad Eye going on.
Pegasus pulling his hair back to show Kaiba his empty eye socket.
Yugi missing with the dagger throw is both funny and this trope.
Two rather distinctive sequences make the movie feel like it's ramped up a bit from the anime:
Yugi's exploration of the Puzzle (which he's trapped in while screaming in pain) results only in doors leading to utter nothingness. Upon yet another door, he stops and screams for the Pharaoh in utter frustration, as the camera pulls back to reveal just how massive and empty the chamber is. The shot was used in the movie's trailer.
Soon after this, Kaiba summons Peten the Dark Clown and attacks the Pharaoh directly. Before Kaiba even makes the attack command, Peten's card vanishes and reappears behind Pharaoh's, after which Peten stabs him straight through the back - and through the heart. The stabbing is silhouetted, but right on-screen.
Yu-Gi-Oh! GX and its Manga
Trueman's and Darkness' (the one from the last arc) monsters could qualify.
The Darkness Bramble, which bursts through Darkness' chest, Darkness Outsider, which is a clown which opens its face to tentacle rape things with its brain, and Darkness Neosphere especially.
The Facial expressions done By Saiou when The Light of Ruin fully posseses him are practically worthy of Rivaling Yami Marik's Facial Distortions.
Yubel. Just, Yubel. If anyone wants to elaborate, they can. The fact that she/He looks like Yami Marik and Yami Bakura's love child dosen't do anything to lower the nightmare factor.
Going into more detail, in the Japanese version it switches back and forth between using a male and female voice, and is a batshit insane stalker that considers love to be sharing of all feelings, most notably pain. So think about this, Judai is stalked by a monster that is not only possessive to the point where it tries to kill anybody else that gets close to him, but considers making his life a living hell a sign of love.
That Jinzo spirit in episode 14 has a terrifying voice. Not to mention his deck is filled with creepy monsters.
Episode 38. Not supernatural or anything, but the sea captain is just downright creepy—no matter whether you watch the original or the dub.
Amon, in the later parts of his arc, does some majorly disturbing things. One of the creepiest moments of all the Yu-Gi-Oh shows for this troper was watching Echo insist on sacrificing herself for him and him accepting so easily.
Especially Kiryu Kyouske. Everything he does in the first duel with Yusei was primarily to further his deck's goal and to attack Yusei with almost sadistic glee. The Dub, while some deride it, is actually quite good at giving Kiryu a very insane laugh and even 4Kids' corny jokes only serve to emphasize his madness.
Divine is a source of this as well, in that he takes kids, basically who are mistreated, and trains them into being psychic weapons. And if your not strong enough to rip your enemy limb from limb, well, You Have Outlived Your Usefulness...like anyone would miss you.
And if you can't survive his experiments to make you strong/useful, you weren't good enough for him in the first place. He'll probably just go and look for a replacement...
And let's not forget how he made Aki his pawn by giving her the 'love and understanding' her parents 'did not' (they simply had no clue how to help her, but surely Divine never suggested that possibility) becoming pretty much her only reason to live. Her hairpin is meant to be a Power Limiter, so let's hope he never tried to talk her into becoming stronger the same way he did to others, like Misty Lola's brother...
Arm in a jar.◊ Don't you want to know what the hand is doing it in the jar?
It is revealed that the arm belonged to Rudger Godwin who sawed his own arm off without any sort of anesthesia.
In an early episode it is revealed that Rex Godwin has a false metal arm. In episode 62, he takes the arm out of the jar, and, with the purpose of absorbing the arm's evil power, attaches the severed arm (which had been floating in that jar for over 17 years!) to his own live upper-arm tissue. This turns him into the ultimate Dark Signer.
Placido and his crew are a wellspring of horror. Who are these strange men in white? What do they want? On a side note, Lucciano's laugh would fit right at home in a When They Cry series...
Speaking of Placido, he has a rather graphic death. How graphic is it? Well, the animators apparently decided that they would subject the viewer to the lovely site of: his spine (which looks very much like a human's) being stretched before it is torn apart. Severed red and blue wires (veins anyone?) are clearly visible sticking out of the centers of both halves of his torn vertebrae. Does him being a robot somehow justify such a blatantly graphic death?
It doesn't help that his dead face gets stuck in an expression of ultimate terror, and it stays that way, shown and zoomed in on several times in episode 110. As if the viewer hadn't be traumatized enough! When he "revives", the right side of his new face is covered with what appears to be tribal-esque marks. Though considering they are violet, they could very well be bruises. Eeeuuuughhh.
ZONE. There's just something horribly unnerving about an either very old or very burned individual (probably the former) under 50 tons of machinery shaped like a comma. His crazy voice and the fact that he resides in a White Void Room just makes it worse. When you think about how mentally damaged Paradox and Aporia were after the ruined future, it's difficult to imagine just how ZONE will turn out as their leader.
Have you seen Jack Altas and Rex Godwin in the 5D's manga? WELL◊ HAVE◊ YOU◊?
Episode 15. Yuma somehow has his mind transferred to the Dark Magician. We get a first-person point of view of the Dark Magician of Blue Eyes White Dragon roaring at the camera.
We also have the situation of IV's ace card, Number 15: Gimmick Puppet Giant Killer. From its creepy, unsettling unmoving face, to the very fact inside its chest is a torture device made to grind up whatever monster it takes inside of it. Fortunately, the character's monsters that were victims were inorganic. Check out how creepy that thing looks here◊. Granted, IV's deck of puppets is eerily unsettling as it is, especially Gimmic Box◊.
and Pegasus, although it's all undone by the time Yugi, Yusei, and jaden defeat Paradox.
Paradox fusing into Sin Truth Dragon. His facial expressions, the groaning in pain, the roar followed by the dragon shrieking, and the face that he refers to it as "himself".
Yu-Gi-Oh! Video Games
DarkNite and Nitemare. They come out of nowhere in Dark Duel Stories, can overwhelm you within turns, and come with broken cards. Their lines are oddly cryptic and Mind Screwy.
And somehow, in Forbidden Memories, they became even worse. Yeah, bet you thought Heishin was the Big Bad, didn't you? Well, he outlived his usefulness, was turned into a card and then BURNED UP. And even if you manage to defeat DarkNite, he transforms into Nitemare, who looks something like a mummy who decided to invest in Magitek.
Let's not forget that DarkNite doesn't die after Forbidden Memories. He only returns to wherever he came from, which makes him more than capable of returning.
...which he eventually does in The Falsebound Kingdom. By manipulating Scott Irvine ( a horrifying madman in his own right), DarkNite creates a giant virtual world that will bring him to the real world. Oh, and he controls all three god cards now too.