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Nightmare Fuel: Yu-Gi-Oh! Card Game
An archetype known as "Gimmick Puppets" is generally accepted as the archetype with the creepiest art. All of the monsters within the archetype are evil looking-puppets, like "Gimmick Puppet Nightmare."◊ Literally, nightmare fuel.
One specific card, "Gimmick Puppet Dreary Doll,"◊ had to be completely redesigned in order to be exported from Japan to the rest of the world. The original artwork is a childlike puppet that is covered in bloody bandages while sitting in a coffin. The new version it still unsettling, but it makes it look more like a toy◊ instead of a dead child.
There is the implication in the story behind the cards that Invader of Darkness is some sort of Evil Overlord who is something like Darth Vader. And that, going by the number of cards searching for him, he probably did something unspeakably horrific. And there's how he probably did in Gagagigo, leaving the poor guy for Kozaki to repair, who probably has a Evil Plan of his own going... yeah, Invader is the Big Bad.
Magic Drain. Naked white haired vampire sucks a guy's blood and it looks VERY rape-ish.
Parasite Paracide. TCG Artwork: a simple insect with a few worm-like tentacles. Very Squickish. OCG Artwork: Same insect, different pose, tentacles protruding from a soldier's face and mouth.
Dark Jeroid has a lot of Vagina Dentata going on, its real head is on its crotch, and one gets the feeling the weakening effect is the opponent monster being squicked.
The trap card Tragedy. In the OCG, it shows a guillotine. In the TCG, it's 'censored' to show a lass who looks distressed, with an evil looking chap looming behind her, from the darkness. Said evil chap has a blood red moon behind him, which happens to be full, which happens to have an effect on him...
Another example, although much less scary than the above, of censorship making things worse is the monster Mystic Tomato. The original artwork makes it look like a Jack-O-Lantern, but in the TCG, its a tomato with a bit-too-realistic monster face.
Some say that the creepiest card in existence is Il Blud.
To elaborate - Il Blud is an evil.... thing with a dark, small face (with glowing red eyes) wearing a jail suit, complete with ball and chain attached to its leg. This wouldn't be so scary, save for the huge fucking rip in its stomach with a giant, distorted face staring at you like something out of a creepypasta!
Many of the earlier cards were REALLY unnerving, but one of the worst was Sorcerer Of The Doomed. It basically looks like an aged corpse with a malevolent expression and a body suit of horrified faces. The flavor text also helpfully states that it is a master of life-extinguishing spells.
Another such card is Doma The Angel Of Silence. What the hell where the creators thinking putting this in a card game aimed at children?
Much of this comes from earlier cards being based directly on Kazuki Takahashi's designs from the manga. Compare the original Manga to shows like Zexal, and you'll realize that the comic treads much, much more heavily into the Horror genre than any subsequent iteration of the franchise.
The Shadoll is successor of the Verz/Evilswarm archetype. They're basically puppets controlled by Elshadoll Nephilim. However, they may be corpses of the fallen. Shadoll Lizard is a puppet version of Satellaknight Unulkhai. Elshadoll Midrash is a puppet version of Wynnda. A pixiv user did a speculative transformation sequence for Wynnda and it is terrifying.
The WickedWorm Beast. Look closely at its card. Is this thing a humanoid monster with worm tendrils... or (more likely) a human corpse being controlled by a monster worm parasite?
Pumpking the King of Ghosts. Can you imagine seeing this thing in a pumpkin patch? A huge one-eyed pumpkin with jagged teeth giving you an evil eye. Shudder.
In the old console games, he's even worse. Take a good look at him in the Falsebound Kingdom.
Necroface has a freaking porcelain horror movie doll with some freaky tentacles smashing out of its face, not to mention that bubbling mass coming out of one of its eyes.
The OCG artwork for Axe of Despair, featuring a grisly looking skull-like face with an axe blade sticking out the side of it. In fact, Dueling Network, a simulator that always uses the original artwork, uses the TCG version of that card.
Dark Hole, which shows an extremely creepy black hole-looking thing. What makes it creepy is if you look close, it resembles a giant eye, which causes Fridge Horror to make you wonder, is this a hole or some other being's eye?
Well, if you look closely, there appears to be stars surrounding it, suggesting that it is an Unrealistic Black Hole