During the fight with Tarkus in Part 1, he decides to grab two hapless townsfolk, and crushes them to paste with his bare hands, before drinking the body juices that came out. We even get to see one of the victim's have the skin on his face tear off near the end of it.
The way in which Dio manages to deal with what happens to him at the end of Phantom Blood is quite shriek-invoking. Long story short, he decapitates Jonathan and places his then severed head onto the headless body.
Would the scene in which he turns that woman into a zombie and calmly watches her eat her own baby count? The woman Dio has brought before him is begging him to take her, but spare the baby. He gives her his word that he will not even touch it. Shortly afterward, the zombie mom does as is said above. He kept his word. But, it once more proves what a monster he was.
The way vampires in this series suck blood - while the normal neck-biting method works, more often than not they'll just dig their hand into someone's neck, causing all of their veins to bulge hideously as they're drained to a husk. At one point Dio grabs Jonathan's carotid artery between his fingers.
The way the Pillar men move, and basically almost everything about them and how they evolve.
Reduced to a brain with blood vessels, Esidisi possesses Suzie Q, resulting in some hexagon shaped eyes while blood bursts out of her profusely in preparation to blow himself up with the three Ripple users.
Alessi is one of the more genuinely terrifying villains in the series. His stand, Sethan/Set has the power to turn those who stand in his shadow into children, so he can have an easier time of killing them. The sequence involving him focuses around his attempts to kill Polnareff, and it wastes no time in showing how powerless and helpless he is as a child. Oh, and he keeps getting a lot younger as the chapter goes on, so there's literally nothing he can do to defend himself. That's not even the best part; that would be what becomes of a bystander woman who happens to run into Polnareff as child, but stays in Sethan's shadow for so long she de-ages into a fetus. She recovers, and things end just well enough, but that doesn't stop the chapter from being very tense and disturbing.
And in the CapcomFighting Game, Alessi is a playable character from the start. And yes, he can use Sethan to turn any character in the game into a child,note (save Joseph, who just reverts to his Part 2 appearance, Khan, who turns into a cow, Dio, who turns into Nukesaku, and Shadow Dio, who turns into Wang Chan carrying Dio's severed head!) but that's not the disturbing part. Whenever someone is turned into a child, he pulls out an axe. Which, yes, does a lot more damage. Also, when his target is at normal age, he's his usual Dirty Coward self and has a particularly fast backdash. When they're children ? It's his forward dash that's faster than usual. The icing on the cake really is his theme, which sounds like the theme of a maniac serial killer.
Vanilla Ice's stand, Cream. It's horrifying to see how it takes out Avdol and Iggy. Iggy might be worse since he gets cut in half and you have to look at his waist stump.
In the OVA, anyway. In the manga Iggy dies by the wounds he sustains from a (literal!) Kick the Dog moment and by protecting Polnareff.
Death 13. To elaborate, Death 13 is essentially the JoJo equivalent of Freddy Krueger: it is a Stand that can invade your dreams and attack you while you sleep, and any harm inflicted on you in the dream becomes reality. If you're killed by it in the dream, you die in real life. And that's not even the worst part about it. The worst part is that its owner, Mannish Boy, is an infant, and when infants tend to play with things, they tend to be rather...destructive.
When he has everyone in the adventuring party pulled into his dream-world, he let's the unreality run free... as in "the fucking flowers and mail-boxes start laughing like the furniture in Evil Dead crossed with a Disney Acid Sequence run free." Shiver.
To make matters worse, his stage in the Capcom fighting game is a carnival with fucking demonic faces adorning everything, and the music is all but fitting for this grotesque imagery.
The stand Empress takes the form of a wart that grows and consumes its host.
Terence D'Arby. There's a reason why he's one of Dio's favourite servantsnote Stated in his character profile in volume 13 (25 if you include the previous parts). He challenges people at video games and puts the loser's soul in a Creepy Doll, much like how his brother Daniel keeps them as poker chips. However, unlike the slightly more sane Daniel who (for all intents and purposes) kills them first, he keeps his victims conscious and aware of their surroundings but unable to do anything but whisper barely audible pleas for mercy. Why? For fun. Some of them have presumably been in this state for years.
Think about it for a second. How scary is it to know an invisible baby is drowning underwater?
Yukako lit a girl's hair on fire, blinded her, and bound her tongue just because she was helping Koichi with classroom chores.
What happens to Masazo Kinoto once Cheap Trick leaves his body...
Yoshikage Kira's "father-son" moment with Hayato. Poor kid.
Yoshikage Kira in general.
Sheer Heart Attack. When it isn't loudly exclaiming "Look at me!", it is completely indestructable, chases whatever the warmest thing in the vicinity is, and the explosion is bigger based on how hot that heat source is. The worst part? Even if you trick it, it seems to know whether it did or didn't kill a human.
There's a corner where Reimi's ghost resides, the only way to get out is turn after 20 feet. If you ever turn completely around at the wrong point, this happens and you're Dragged Off to Hell. This is Kira's ultimate fate.
That rat Jotaro and Josuke look for. It has the ability to fuse bodies together like gelatin, while they're alive. An inconspicuous rat of all things. Or rather, an inconspicuous pair of rats.
If you are scared of Spiders, it is NOT a good idea to read the Debut Chapters of the Aerosmith Stand. Just... skip it...
Once you see how Illuso died, you can thank Araki for deciding to shelve Fugo...
The Clash and Talking Head arc was scary on a psychological level. Knowing there's a killer mini-shark hidden in the water your friend is about to drink and only able to tell them it's fine to drink.
Carne's stand, Notorious B.I.G., a horrific, carnivorous blob that will devour anything that it sees (unless softened by Trish's Spice Girls Stand). The worst part? It can't die. The heroes can't kill it. They have no way of ever killing it. They can only drop it into the ocean and render it mostly harmless, but the narration states that it still attacks passing ships.
And the reason it can't die? Stands aren't vulnerable on their own. To defeat a Stand, you must defeat the Stand user. This thing broke out of its user when the guy DIED - it can't be killed because there's nothing to target. Given that Stands are in part a reflection of their user, what does that say about him?!?
Cioccolata is this all by himself.
He's a doctor who purposefully botches surgeries just to see what would happen, then films it to watch it again. He also knows exactly where to cut to dismantle a person without killing them, which is how he comes after Giorno as a bunch of detached body parts hobbling towards him.
Scolippi's Rolling Stone stand shows him how people die. If they touch it, even on accident, or accept their death and do so, it tells them a way to get a more peaceful and meaningful death—which they'll promptly embark on. When it showed his girlfriend how she'd die, she took the peaceful suicide it suggested would also help her father via organ donor. This, though, caused her father to attempt to send assassins after him. He handles this pretty well for a Messianic Archetype.
The crimes for which a lot of the inmates were incarcerated are often all too reminiscent of real cases. Etro (F.F.'s original body) kidnapped a child merely to fulfill a childhood fantasy. Kenzo founded a religious cult (its ranks including some celebrities) and instigated a Jonestown/Heaven's Gate-esque mass suicide. Annasui caught his girlfriend in bed with another man and literally took them both apart.
The way Guess uses her ability is beyond messed up.
If you thought Steely Dan's ability to transfer damage done to him onto your grandfather was bad, imagine being targeted by Xander McQueen's Highway to Hell. It inflicts all of Xander's wounds on you, and unlike Dan, who uses Lovers as a deterrent, Xander is actively and violently suicidal.
Remember Ungaro and his Bohemian Rhapsody? That's probably the reason Araki was never picked as an artist for Disney. Considering how the Dwarfs and Pinocchio turned out◊, we should all be glad that Mickey jumped ship before we could really see him.
The mother goat. Just... the mother goat...
The Stand Yo-Yo-Ma secretes a flesh-dissolving acid from its mouth. It fills Jolyne's tongue with holes to prevent her from warning Annasui.
Heavy Weather's entire arc is pretty unsettling... and might bring up old memories to people who've read Uzumaki prior to this...
Emporio, under the influence of Jail House Lock, being unable to move from a electrocuted puddle because he's stuck in a constant loop of remembering what he's supposed to do.
Pucci's C-Moon has the ability to reverse an object's gravity. This represents in the object turning inside-out. It happens to Jolyne's hand.
To elaborate, the stand simply turns things into dinosaurs. Neat, right? Well... except it sometimes leaves the user with an ear-to-ear Glasgow Grin when back in human form, which leaks while he drinks!
Ringo's backstory. His entire family was killed in one night while he was sleeping and the same killer tried to rape him and make him his "son".
Axl R.O.'s Stand, Civil War, in Steel Ball Run's Chapters 56 and 57, which attacks by manifesting the guilt and sacrifices made by the opponent and fusing with their bodies. Hot Pants and the body of her deceased younger brother, Johnny and 'Danny', etc.
Lucy carrying the Saint's corpse in her womb.
And her glass-like stand replacing her skin after she fuses with all the parts.
The whole process of fusing with the corpse parts is pretty unnerving.
D 4 C. The President's stand. It has the ability to travel to parallel worlds, and bring people back to and from them. If two alternate universe selves meet, then they collapse into Menger Sponges, and cease to exist. This happened to Wekapipo.
The art for Steel Ball Run is beautifully detailed. That also makes the copious gore (remember that this is when Jojo transitioned from shounen to seinen) even more unnerving. Especially when a steel ball meets a (deserving, but still) face and all the chunks of skull and teeth come flying off, maybe with an eyeball as well.
Josuke taking away Joushuu's sight, leaving two blown out voids where his eyes used to be. It didn't stay that way, but still.
The whole scenario of being trapped in a booby-trapped hallway and losing control of your own body is damn terrifying.
Kira made someone eat his own fingers. How? He just told him to do it.
Daiya has the power to take away memories, which is already horrifying, but these memories manifest in the form of chess pieces that fall out of her target's body. Not to mention Daiya is a 16 year old immature girl.
Rina's disease where her skin stiffens up and folds like origami. It's healed by the Holy Corpse, but then her son gets it due to Equivalent Exchange.
Made worse when Yasuho gets the same disease.
The discombobulating effects of Tsurugi's Stand almost get Yasuho raped. Twice.
During the fight against Yagiyama, Josuke and Norisuke IV have to escape from chestnuts. Sounds boring, right? Well, the Stand they fight causes a center of gravity in their bodies, drawing in surrounding objects. The spines of the chestnuts fly off them, and into Josuke's fucking eyes.