Carl King was the worst bully Peter ever had, and after seeing Peter be bitten by the radioactive spider, Carl eventually put two and two together, tracked down the now dead spider, and ate it in an attempt to give himself superpowers. He became a colony of arachnids that could invade people's bodies, devour their innards, and wear their flesh like a suit. Most of his victims (which included his own parents) were women and children. The arc was full◊ of◊ nauseating◊ Body Horror. Yeah, he's the page image here. For good reason!
He also possibly killed his dad while disguised as his mom while they were intimate. Did we mention this guy was created by Garth Ennis?
On the flip side, the almost casual way he's permanently dispatched at the end of his story was immensely satisfying.
Monster Ock, which is basically what happens when Doc Ock gets Carnage's symbiote. There's no way to defeat him: all you can do is run, and pray he won't catch you, all while he makes noises that sound like a monster being strangled. Look up videos of him on YouTube, and many of the comments will be similar to: "This scared me to death as a kid!"
A few of his growls end in an inhuman "DIIIEEEE!!!" that sounds not too dissimilar how the alien says it in Independence Day. About halfway through the chase, Doc Ock's human voice returns to simply say, "NOT... OVER... YET!!!!"
The sequence takes place in a vent, meaning that you may get stuck to walls running from him and wind up seeing the meter that shows how close he is to you shoot up fast. Try NOT to feel your heart rate spike.
How about Carnage himself? Him shrieking "The pain, the paaaain!" every time you pull him into the sonic emitter area...
Similar to Monster Ock, there is Spider-Carnage. Imagine your favorite childhood character, turned into a horrible monstrosity that wants to kill everyone.
At one point, Carnage infected the Silver Surfer. The implications for the universe are horrifying.
Speaking of Spider-Man, the Tordenkakerlakk from the graphic novel Hooky is worth mention, due to the myriad of grotesque forms it takes throughout the book, for the sole purpose of stalking a little girl who has been alone for 200 years.
The Amazing Spider-Man story arc "Shed" is this. There's no return to Curt Connors for the Lizard. Not now. Not after what he does.
And the worst thing - Lizard is now gone, probably for good. And Curt is stuck in his hideous form, well aware of what he had done.
Two books published by Marvel about the villain Carnage, Mind Bomb (which is by Warren Ellis by the way) and It's A Wonderful Life. The character of Carnage is already up there to begin with, having been in prison serving eleven consecutive life sentences for murder before obtaining the symbiote, and after obtaining it, his only goal was to kill as many people as possible. The entire plot of Maximum Carnage was that Carnage wanted to kill everyone in Manhattan. He's a killer with no style or gimmick, who only wants to kill, preferably by brutal, gory means. But these books... both involve Carnage using the symbiote to connect to the minds of other people, which allows us to see what's in Carnage's mind. He lives in a world of corpses, willing victims, dark humor, and frightening landscapes all of which house his knowledge, desires and memories of the past. There is even a special area where Carnage spends time hacking up Spider-Man copies for fun. One panel of Mind Bomb shows the "real world" as he calls it, which features a man eating intestines and holding a cup labeled "urine sample" as a drink glass, an elderly woman in bondage gear, and a cop with a KKK hood shooting a man. In Mind Bomb, the man he's connected to, Dr. Matthew Kurtz, goes completely insane from this experience. The second book plays more to Cletus Kasady's history as Dr. Kafka and John Jameson are connected this time, each mutating into a vicious creature (John turned back into the Man-Wolf, a previous villain form, and Dr. Kafka slowly changed into a cockroach) finally ending when a young black kid named Billy shows up deep within the area of repressed memories. Carnage threatens to kill him if they get too close but seems unable to (it's hinted that Billy was a childhood friend, but the details beyond this are never really said) and finally has a breakdown, releasing the two but left in a catatonic state. The artwork is graphic even for a Carnage story and the cover of Mind Bomb has him perched on a pile of human skulls. The oddest part? Both books were approved by the CCA. Even worse, IAWL seems to play with the idea that the people running the mental hospitals that house supervillains may actually be more evil than Carnage. Mind Bomb showed him as oddly intelligent for a supposedly uneducated guy but IAWL opens with Carnage ranting about the change in management. He even seems to be more than aware that many "accidents" that are resulting in patient deaths during their transfers are intentional and even calls out that the car crash that killed Wolverina (not Wolverine) was on purpose. This alone might be the most frightening aspect, Carnage himself calling out someone else for being worse than him and being right.
Kraven's Last Hunt. Kraven the Hunter literally buries Peter alive and assumes the Spidey identity, only going extra rough on criminals while Peter's friends and family have no idea where he is for days. The What If? issue was even worse, with Kraven actually killing Peter, and later digging up his festering remains in order to consume them.
"They said my mother was insane..." *BLAM!*
The sequel The Grim Hunt, which served as the finale to The Gauntlet series of stories (revamps of old Spidey villains into scarier threats), is a mix of Psychological Horror, Body Horror, and good ol' fashioned Gothic Horror as Kraven's family goes about attempting to raise their patriarch from the dead through Blood Magic.
In a story arc titled Venom: Shiver, set in the isolated Alaskan wilderness, an army base loses contact with a nearby military research facility in the midst of a driving snowstorm. One of their officers, a young woman named Pat, takes a long and lonely journey through the storm to find out what's gone wrong. What she finds is a dark, cold, silent facility filled with the mangled corpses of the staff, most covered not only with blood, but also a familiar-looking black sludge. Only a single, nearly catatonic survivor remains. She chooses to take the terrified man back to her base, followed by by a lone figure obscured by the snow. While the overarching plot of the story is, admittedly, pretty weak, and borrows very heavily from The Thing, what follows in the next several pages still manages to be a pretty unsettling look at what the Venom symbiote gets up to when it doesn't have a host like Eddie to moderate its violent impulses . . .
The Venom suit. An organism capable of sentient thought that relies on other organisms to live via a symbiotic bond. It affects you not unlike a drug, altering your state of mind and making you crave its power. While it provides benefits to you, it also uses your body against your will as it pleases and takes a toll on you in the long run. Once removed, some fragments of it retain inside the blood, as the rest retains not only the thoughts you shared, but all of your memories, that it will then share with its next host. It holds a grudge, will crave blood when it wants, and has an obsessive personality towards former hosts. Not to mention the powers it grants to its users, ranging from claws to tendrils.
Spider-Man can be pretty damn scary when he's angry. Take when he caught the Sin-Eater. Stan Carter has been going around killing people, including Spidey's friend in law enforcement Jean DeWolff, so Spidey wants him bad. After saving first girlfriend Betty from being killed, Spidey disarms and smacks Carter around... but he just doesn't stop despite Carter's pleas. Every couple of panels cuts back to Betty witnessing this and looking terrified. Spider-Man nearly beats a man without super-powers to death and probably would've if not for Daredevil stopping him.
Similarly, any time Spidey himself mutates into a Giant Spider.
A Spectacular Spider-Man (comic book) arc features Spidey and Black Cat stopping Ock from nuking New York. While the bomb is stopped Ock's tentacles bind Black Cat and one shoots her with a machine gun. That's disturbing enough but Spider-Man tears out several of Ock's extra arms and the issue ends with Ock on an operating table, refusing pain killers while his arms are reattached to him, vowing to return the pain to Spider-Man.
The fifth Green Goblin (who wasn't human, but a genetic construct) revealing his empty face, and then gruesomely melting into a pile of goo after assuming Harry's appearance.
The Amazing Spider-Man #373. Venom is held in custody, with a jerkass guard who's favorite pastime is intentionally turning up the sonics in Venom's cell so he can laugh at Brock and the symbiote's agony. Once Venom escapes the cage, he wraps his tendrils around the guard's head and squeezes. And squeezes. And squeezes. His head is completely covered in tendrils but we see it gradually getting smaller and smaller. And then we cut to the other guard's horrified face as Venom cheerfully sings "Pop goes the weasel!"
A lot of people think of Mysterio as being a minor Ineffectual Sympathetic Villain at worst. Those people really don't realize how horrifying ol Fishbowl can get when he get's serious. Old Man Logan kindly shows this. The Xavier Mansion is being attacked by an army of supervillains. Wolverine can't find any of the other X-Men and the villains are threatening the students, so Logan is forced to pop out his claws and kill them to protect the kids. Finally he gets down to Bullseye and stabs him when suddenly Bullseye says "Why Logan?". The illusion drops revealing that the whole time Wolverine was slaughtering the other X-Men. Bullseye is actually Jubilee, who is basically the closest thing to a daughter Logan has ever had. Mysterio than appears behind Wolverine, casually mocks him for thinking he could take on that many supervillains at once, and than walks away, having totally broken Wolverine in mind, body, and spirit. Really, Spider-Man is incredibly lucky that mainstream Mysterio doesn't have very big ambitions; the Wall-Crawler wouldn't last a week.
The Spider-Woman (Mattie Franklin) villain Flesh had no bones, and possibly no other innards, due to a curse, and was thus a prime source of Body Horror. Mattie (who was once sewn inside Flesh) noted that she and her sister, Bones, likely made their getaways while the witnesses and responders to their crimes were busy throwing up at the sight of them.
Any appearance of Norman Osborn between "The Final Chapter" (where his already notorious insanity was magically enhanced) to his appearances in The Pulse and Marvel Knights Spider-Man (where he was finally outed as the Green Goblin and sent to prison) was full of this. His MO by this point was to straight up torture Spider-Man in any way he could to mold him into being an Osborn worthy of his legacy. This included such lovely acts as brainwashing Peter into being the Green Goblin without even realizing it, using electro shocks to force Peter to choose darkness over light, causing an alcoholic relapse in Flash Thompson before engineering a car accident into a school via tanker truck with Flash, and generally threatening his loved ones through surveillance photos and the like.