Depending on the alien Ben is turning into, some transformation sequences can involve a large amount of Body Horror:
Heatblast has Ben's skin being gradually covered with rock then being set on fire;
Ripjaw show's Ben's mouth distorting itself and growing monstrous teeth;
Fourarms, XLR8 and Wildmutt in the original series have Ben's muscle growing in a quite disturbing way, making it look like his nerves are becoming apparent;
Ghostfreak has Ben's head turning into a skull during the first part of the transformation; it's even worst in Alien Force, where we get to see his spin distorting, his claws emerging in a Wolverine-like way from his hands, and his skull making a 180$ turn;
Goop has Ben literally melting into a pile of goo.
Eon in his first appearance was damned creepy. What do you do when a Time Master doesn't like you? Basically, run. His time ray causes Rapid Aging, and the first guy we saw him used it on looked like a half-decomposed corpse... and was still alive. His body had become so brittle that at one point, a not-very-hard touch causes the guy's arm to break off (and we learned his ability to feel pain was very much intact.) You probably sighed with relief when the poor guy finished his exposition and died. There's also the way he stalked Ben: staying out of step with reality, he could follow Ben anywhere unseen. You know that weird little blur in your class picture? That's him. Watching you. It's hard to describe, but the handling of him when he'd approach Ben was more like a horror movie's supernatural foe than one of Ben's standard enemies. Also, when he's around, no one can help Ben, because Eon is fond of Time Stands Still. You and a bunch of heavily armed Plumbers are getting ready to show this guy who's boss... and suddenly Robert Picardo starts to talk... very... slowly. Then you're the only one moving... you, and the guy responsible for the most Family-Unfriendly Death in franchise history, who hasn't done it to you yet because he needs you, and who's been looking over your shoulder at school and at home and everywhere. Unlike Vilgax or Diagon or any other Big Bad, there's not an alien in Ben's arsenalnote Okay, he'll eventually get Clockwork. that makes Eon less of a threat. Every time Ben encountered him - and all the times Ben had no idea he was there - Eon could have killed Ben at his leisure and there'd have been nothing Ben could do. His plan needed Ben alive and that's why Ben is still here.
When he returns in Ultimate Alien he's using his power to its maximum level, outright turning to dust anything he hits with it. He also gets a reputation as Hero Killer - he's hunting Bens one parallel dimension at a time, and ours is just next on the list. (It turns out they're not dead, though: his Mooks are the alternate Bens, brainwashed.) Ben gets lucky in that his alien forms leave his human form behind unharmed if they get dusted, though he loses the ability to transform into that alien. (They're restored, though.) He's no longer getting the horror movie treatment, but you still hold your breath with him.
It's kind of a scary world to live in because of how easily it seems the world is doomed. One xenocyte? Your whole world contains nothing but DNAliens in short order. Death Star class ray guns are available to even comedic villains. Many planet, including Earth, are considered so insignificant that the Plumbers will sometimes not even bother ensuring security to protect them, meaning few people would lay a finger if someone suddenly decides to conquer or destroy Earth (even in the light-hearted show Ben 10: Omniverse, a character treatens to destroy Earth because a guy living on it won't marry his daughter, and encounters no resistance whatsoever).
Vilgax can be quite terrifying from some angle; his voice, provided by Steve Blum, is creepy by itself, especially when he is mostly seen in the shadows in the first episodes. When he finally ends his treatment and goes after Ben of his own, he proves to be unstoppable, defeating most of Ben's alien forms with nothing else than pure strength. And add to that he was ready to cut off Ben's arm to get the Omnitrix.
Even worse, in the alternate universe episode "Gwen 10", it's made clear he doesn't need to cut Gwen's arm to get the Omnitrix (unlike canon Ben, who had the Omnitrix long enough for it to bond to his DNA). He just prefers doing it that way because it's more fun for him...
And then the movie Secret of the Omnitrix reveals he destroyed a planet just for the sake of testing his newly acquired toy.
The Limax appeared only once, but the one times we saw them, they were creepy like hell; those creatures kidnap old people to take their place, while retaining their classic reflexes. Seeing those old people twisting their bodies in weird ways, showing fangs and hissing like snakes could actually fit in a horror movie. To make things worst, it's clearly stated they were intending to eat the humans they had captured.
Kevin 11; the character initially appears as being a mere punk with powers... until we find out he is ready to kill thousands of people just to get money. The Slasher Smile he displays in some scene also contribute.
The Slasher Smile is what really sells it. The joy he has when he's about to kill someone (stopped by Ben at the last moment, naturally) makes it clear that he loves hurting people, to a greater degree than any Big Bad the series has had. This also adds Fridge Horror to it: when he's onscreen, he's always stopped when one second away from killing people because he can... and he is sometimes active offscreen, when Ben's not there. (Watch Kevin's onscreen behavior in "Framed" and then recall that he operated with the same MO in several other cities before Ben and the gang found out what was going on. There's a reason people are complaining about the improbability of his Heel-Face Turnto this day.)
Then it turns out his powers allow him to copy Ben's powers by absorbing energy from aliens, resulting in some scene into large Body Horror; his final mutation in "Framed" is one of the creepiest scene in the show; we can feel the pain he goes through while the whole thing happens.
Zombozo; not only is his look disturbing, with a zombie-like face and a long, inhuman tongue, but the guy feeds on people's happiness. Not scary so far? Well just see what is left when he has sucked most of it...
The place where he's fought in the end makes it worse. Basically, it's like being inside a Disney Acid Sequence, only significantly less cute. The guy is supremely creepy, especially because this is usually a sci-fi show. This guy isn't an alien, or someone who got this hands on phasers. He's a Humanoid Abomination who steals happiness and creates a bizarre netherworld with Alien Geometries at his command. Everything about him takes the subverted cuteness that makes a Monster Clown up to a cosmic, reality-bending scale, and we never find the man behind the curtain, never get the "ah, here's his Holodeck-maker" or "'stealing happiness' means his Applied Phlebotinum does this or that to your brain chemistry" Doing in the Wizard moment... and it also doesn't work like any magic we see with Hex and Charmcaster (and Gwen, once she steals Charmcaster's book). He doesn't play by the rules we know, he and everything about him simply is. He will feed on your very soul. He will turn your reality outside in. How? He just does, it's just what he is. If HP Lovecraft had created The Joker, you would have this guy.
What's worse is how he was beaten. Ghostfreak. All we see is Ghostfreak's back to the camera as he pulls apart his body to reveal a mass of tentacles to Zombozo. It was only a taste of what was to come. (Not to mention... Ben has a form that a Humanoid Abomination is afraid of?!)
Clancy in his first appearance; not only is the guy controlling bugs, which is already creepy of its own, but he intended to have a woman eaten by them.
And in the "Negative Ten" special, he has been turned into a half-human, half-bug monster. He hasn't shown up since, so we never find out if the change is permanent or not.
Anything related to Ghostfreak; from his creepy transformation sequence, to the nightmares he made Ben go through when he was attempting to escape, to his true form, to his scheme in season 3 covering Earth with darkness and turning everyone on the planet into monstrous mutants and to top it off, his laugh!
Just think for a second. You're a kid with superpowers, able to shape shift. Now, one of your forms, which you've always been wary of, has suddenly become the subject of screaming nightmares. NOW, it takes over your body and uses it to ruthlessly beat down a trio of villains (it's unclear whether or not Ben was conscious for that). And THEN, it pops up in the real world, giving you a mother of a jump scare before RIPPING OFF ITS SKIN. AND THEN, it goes on a rampage and possessed your cousin, forcing her to fight you and threatening to make her jump off a building unless you surrender. AND THEN, you're forced in a demonic hide-and-seek game while you're two inches tall and it can pass through walls. AND THEN, just when you think it's all over, just when it seems like the nightmare is finally over..."I LIVE!!"
The entire episode with the the alien tick trying to devour all of Earth. The tick has already destroyed previous worlds, and you can see what it does to a planet as it feeds- mutate the environment into a completely inhospitable wasteland. It gradually poisons Yellowstone Park to the point plants have turned into living tentacles with mouths, Old Faithful becomes a sickening pustule of acid geysers, and the the atmosphere turns chalk white. Ben can't harm the tick with any of his current aliens, practically skipping Grey Matter because it's so pitiful. Worse, this tick engorges and grows as it feeds, secretes blue pus, is infested with lice, and sheds its skin to transform into a paler, nastier version of itself.
The nastiest scene is its death. Ben has acquired his first new alien, Cannonbolt, but the tick can't be harmed on the outside. Instead, Ben, as Cannonbolt, goes inside the tick and demolishes its inner organs until they leak out alien blood, smashes through all its ribs, and causes it to explode, spilling its goopy entrails everywhere. Fortunately, Yellowstone reverts back to normal, but there's still the matter of cleaning up the mess... poor Ben.
Just imagine if this incident spread out past Yellowstone and caught the attention of the world. They might not have been able to stop it from wiping out the planet. One also wonders if others in Yellowstone park witnessed the destruction. Plot hole, anyone?
We commonly hear of Ben's exploits on the news and such; "those alien heroes" are well known before Ben's secret identity is exposed in Ultimate Alien. It's not like the world's unaware of all this stuff, even though this incident doesn't get directly mentioned. Of course, with Yellowstone turned into a Death World, it's entirely possible people saw but just didn't survive to report.
The Tennysons go to a wedding between a Plumber family's son and a nice girl who happens to be from a species that despises the Plumbers, and are basically oozes that can look human. When the girl's parents reveal that they have been trying to sabotage the wedding because they can't stand the thought of their daughter marrying a Plumber's kid, they not only turn into huge, bruise-colored monsters, but Ben uses Heat Blast to cook them until they turn to stone, which apparently doesn't bother their daughter one bit. Even Ben's dance with the flower girl gets creepy when her feet turn to slime in the middle of their dance, which she thinks is funny as hell.
In the episode "Last Laugh", Ripjaws deals with a robber by pulling him underwater. The robber isn't seen again.
Damn near the entirety of the episode "Camp Fear". The title alone should have clued you in.
The DNAlien are creepy on their own to an extent, but what can really be scary is the way they are created: the Hightbreeds use Face-Hugger-like creatures to infect humans, turning them gradually into them. Which would mean each time the heroes kill DNAliens, they are actually killing human beings (and it does happen);
The episode introducing Darkstar was downright creepy; the episode starts with a scene of a schoolgirl running at a house and desperately calling for help. The door open, we get something that looks like a Gory Discretion Shot, and cut to the girl walking around in the street, now zombified.
It's then revealed multiple girls suffered the same fate. As the protagonists try to figure out what happened with the help of who seems to be the local superhero. Eventually turns out said hero, despite possessing light powers, is the responsible: he charges his powers by feeding over energy from schoolgirls he seduces, eventually turning them into zombies slaves that he relies on to feed him even more. His habit to drain energy from them is played subtily like rape. To make matters worst, he succeeds in draining Gwen.
And then his zombies slaves turn on him at the end, draining most of his energy and leaving him weakened with a zombified face. Granted, he deserved it, but that was still creepy.
The Gauntlet has Cash, oridinary a relatively harmless bully, starting to use a Techadon hand as a gauntlet, using it as a toy initially. Then the gauntlet gradually takes over him, causing him to become completely psycho and attempt to kill Ben as a revenge for making him look ridiculous in front of his class. And the gauntlet starts gradually rebuilding the Techadon around him, starting with his arm then covering his body then his head... he is saved eventually, but had it not be stopped, he would have probably been permanantly mutated into a Techadon.
The Highbreeds could be creepy on occasions, especially the one who was about to punish Simian at the end of his debut episode. Ben tricked Simian into carrying a DNA alien ear cleaner, which unlike human ears, need acid to flush out... and the Highbreed now has it in his possession:
Simian: T... this is a horrible mistake!
Highbreed: It sure is. We distinctly told you to bring the crystal. Maybe you misheard us. Maybe you need to have your ears cleaned... (loud hissing noises come from the acid dripping out the ear cleaner offscreen as the episode ends)
This was retconned as the Hightbreed merely imprisonning him Ultimate Alien, but still creepy...
Ghostfreak comes back, and now possess additionnal, new powers. He is somehow able to provoke a mass-possession of his own, turning all inhabitants of Vilgax's home planet into his minions as part of his Hive Mind. The planet is then infested in a Xenomorphesque way, with cocoon all over the place. It gets so bad that Vilgax went as far as ask Ben's help.
And then Ghostfreak succeeds in what he had been trying all along: possessing Ben.
Reirassic III's debut- he had his arm severed by a desert parasite, complete with indigo Alien Blood dripping out. Luckily, Ben infused Swampfire's regenerative plant cells into the Highbreed's detached arm and reconnected it to his body- but even so, his arm became a hybrid of flesh and chlorophyll, turning it completely green, along with all the neighboring arteries and veins hooked into it where the chlorophyll eventually melded with the flesh. Kinda cool-looking, but also scary.
There's also those water-absoring tentacles that pop out of his chest when he opens a few skin flaps on it- yecchh!!
Highbreed Supreme is especially disturbing to look at- initially. Pale, fat, and with a face even more covered in horns and deformed than the usual Highbreed. The most disgusting part of him is his belly, which has what appears to be a cancerous mutation on it because he and his race can no longer breed. It disappears after Ben infuses him with Omnitrix DNA, apparently healing the deformity and causing him to turn red and appears more pleasing to the eyes.
In Save the Last Dance, Big Chill keeps possessing Ben and making him act very erratic. When Ben tried to turn into another alien, he transformed into Big Chill, his eating habits and personality go 180—Ben acts much nicer toward Kevin and was shown eating through 2 pickle jars (juice and all) and Big Chill took over Ben to transform. When in Big Chill form, he becomes aggressive, devour metal, growls and attack people. The similarities to Ghostfreak was very frightening even as it's revealed that Big Chill was doing that so it could reproduce.
Time Heals gives us an Alternate Future where Hex and Charmcaster killed Gwen and took over the world. While the scene of Bellwood being invaded with Charmcaster's golems is bad enough, we also get to see what they did to the two other heroes: Kevin was forced to absob the substance the golem were made of, resulting in him becoming Charmcaster's personnal slave. As for Ben, we get to find him in jail, in his Spider-Monkey form.... suggesting they were keeping him alive and forcing him to shapeshift just so they could torture him in his various forms.
Aggregor; the guy is probably one of the most competent villains in the whole series, maybe the whole franchise; He did nothing but win for all his story arc, usually using the protagonists as pawn. And he was ready to absorb (which might as well be kill) five aliens in order to get their powers. Even worst, his final plan was to absorb a Celestiansapien child. This guy was in many way similar to Kevin 11 in the Ben 10,000 future where he didn't reform.
And when he finally get defeated, it's done at the cost of Kevin's sanity, causing to turn evil again and become even more Axe Crazy than he already was in his youth. He starts with just chasing people who causes him harm, initially just to beat them up, but then to kill them; by the finale episode, he completely snapped, now craving for more energy and power, and starts attacking allies and enemies indiscriminately just to absorb their powers. He almost acts like a drug addict, and his chasing of Gwen starts to sound like creepy stalker much like Darkstar.
Not to mention the fact that Ben as Echo Echo only survived him by having one of his selves hidden. Ultimate Kevingenuinely thought he was killing Ben and didn't hesitate a second.
Zombozo shows up again, and while losing the source of his power has brought him down from "omnipotent god of Monster Clown-ness," he compensates by acting in a completely Axe Crazy, Joker-esque way. When we meet him, he'd just come back from burying some henchmen who'd displeased him. He kidnaps Ben's mother and places her in a deadly trap so she would die gruesomely while Gwen was watching, and attempted to shoot at Ben with acid. Worse is how Gwen punishes him for attacking their loved ones- it scares him enough to return him to his stupor he was in after Ghostfreak spooked him. The scene shows us Zombozo screaming in despair, then cut to a fast forward showing Gwen and Ben's mother waiting. When asked by Ben and Kevin what happened to Zombozo, she merely replies they "had an agreement".
In Omniverse, he returns, but he's only got one eye visible... which implies Gwen blinded him in that encounter.
Inspector 13's really, really, really horrible Evil Laugh. Even Ben is creeped out.
Captain Nemesis wasn't much more than a Silver age superhero parody turned evil in his first appearance; yet, you won't laugh at him anymore in his next appearance, where he gets to be the first character in the franchise to succeed in killing innocent human beings. Several times. With at least one body shown (though from behind). And this is supposed to be a kid's show?
Well, when you undergo plastic surgery via the hand of someone best described as an IgorExpy, there's bound to be a line that gets crossed... namely, Gwen catching the leftover scent of the man's blood in the operating room. We get a Gory Discretion Shot, of course, but the cast knew he'd gotten a back-alley surgery because there was just that much blood left over. (As for the good doctor? We find him in a freezer case, quite dead.) There are a lot more deaths kept offscreen. Omniverse hints that he might still be out there. (Of course, as a Lighter and Softer series, he'll probably be more like his first appearance than his second if he does. Then again, Omniverse did give us Malware.)
In "Perfect Girlfriend", Elena turns into countless nanochips and goes into (transformed into Ultimate Echo Echo) Ben's mouth to his lungs as if she was really willing to kill him...
In The Ultimate Sacrifice, Ben is trapped inside the Ultimatrix with the Ultimate Aliens come to life. Somehow they've become sentient and believe that he is keeping them prisoner and using them as desired, and are not happy with it... and they believe Ben's death will free them. You're treated to a scene of a flaming pit where Ben is going to be tossed into to roast alive, as several of his alien forms stand around chanting "Burn! Burn! Burn!"
"Night of the Living Nightmare" as a whole, especially the part with Hex suddenly appearing behind Ben on his car's backseat...
And then we have the final scene showing us Albedo's nightmare, where he is hiding, desperately screaming of terror as all of Ben's aliens are advancing toward him...
The whole idea of the dream eater is kind of scary. Imagine the most scared you've ever been during the worst dream you've ever had. Now imagine a creature that is capable of putting you back there, and keeping you there 24/7 indefinitely." Ben and company had to call a Galvan doctor to Save the Villain because there's no way to remove it without your face going with it - and Galvans are the smartest race in the universe. That means if you ran into this thing in the wild, there would be absolutely nothing you or anyone would ever be able to do about it; Earth doesn't just not have the means to remove it, the human brain may be incapable of the smarts it takes to develop such a thing. Pretty much any And I Must Scream scenario is scary, but this one makes damn sure'' you're gonna be screaming. Forever.
Diagon; his minions, the Lubracas, are weird demonical creatures with the abilitie to brainwash humans merely through physical contact. And they are just bugs compared to Diagon himself, who when he shew up converted almost all human beings into his minions, defeated Ultimate Way Big and gave a Family-Unfriendly Death to King George, by striking him with lightning, stripping him of his immortality and turning him to ashes.
Simian is accidentally responsible for infecting his planet with Xenocytes- y'know, the nasty parasites who mutate anything they feed off of into a Dnalien? Just think of the Dnaliens you've seen up until now, only as monkeys with four arms. Surreal and scary, huh?
In case Zombozo wasn't creepy enough in the original show and Ultimate Alien, Omniverse gives him a more zombie-like appearance, with visible ribs, an apparently missing eye and decayed flesh in some places.
Psyphon has become much more creepy and threatening, with a newer, more shark-like design, Ax-Crazy tendencies (he thinks about eviscerating one of his own henchmen), and actually managing to screw around with Ben's nerves.
And in the mainly fun episode "Special Delivery", he charges himself up with a Dwarf Star and beats the crap out of Humongosaur. Ben is suitably worried.
Khyber's Trophy Room is filled with bodies and bodyparts from various aliens that have been confirmed to be sentient over the course of the show. This includes an Ultimate Humongousaur skull, Grimlock's sword, a Terraspin shell and many others...
Khyber himself has his moment. In It Was Them, when Ben is being trapt by one of his pet's forms, he is shown holding a long knife and saying "Soon", strongly hinting he was intending to behead Ben...
Then In Of Predator and Preys, he outright states he plans to cut off Ben's hand and to keep it with the Omnitrix, even indicating where he plans to place it in his Trophy Room. Even Ben seems disturbed.
Malware's birth in Azmuth's flashback; when Azmuth disconnect the Helix, a yellow and black Galvanic Mecamorph matter emerge from it, shaping itself into him. He then displays his ability to copy tech, seems weakened.... and rush his claws at the closest innocent Galvanic Mecamorph around. And then the flashback cuts off.
Malware's appearance in Predators And Prey showcases that he's got a new, much more monstrous look to him, and it's shown that he, along with his associates, forced Phil, Max's old partner, to use the Nemetrix, with this experiment being shown, but scarcely seen.
Malefactor reveals the reason for Malware's monstorous appearance and all but demostrates his Knight of Cerebus status. When he and Present Ben meet for the first time, Ben is furious and a bit scared at the sight of him. Now keep in mind that Ben himself stated that he's faced many foes such as Vilgax the Conqueror and Diagon the DestroyerWhat has Malware done to make Ben of all people scared of him? Malware even hinted at it, saying something to the effect of Ben knowing better than anyone what Malware is capable of. Chances are, he wasn't talking about the worst thing he'd done in that episode to that point (serving as a distraction so Khyber could scan this alien moth animal for the Nemetrix.)
We also find out what his Arm Cannon does. Malware assimilated a gun that takes an enemy apart on the cellular level, and the effect can spread to anything with a similar genetic structure. If it were to hit a human, every human for 100 miles would basically turn to dust. It also means if Malware ever scores a direct hit on Ben or any other of our heroes, there's no Only a Flesh Wound, no "just stunned." No possible effect other than "you die, game over." Malware's no Zombozo, but every single time we see him, we add to the list reasons why you know if he's around, shit just got real.
Malware endangering a busload of innocent children to escape from Ben is quite frightening. Especially right after the Sandy Hook massacre rendered endangering children Too Soon.
And we finally find out why Ben's so afraid of Malware. He painfully tore Feedback out of the Omnitrix and destroyed him. As if that weren't bad enough, there's how he did it. Red lines spread over Feedback before he's torn out, hanging limply in Malware's hand before Malware causes him to wither and disintegrate into dust right in front of Ben! So on top of all the other reasons this guy is so scary Ben knows he can destroy his aliens in a horrific fashion if he ever gets the chance. No wonder Ben's scared of him.
And it's also a traumatic experence for Ben. It filled him with such rage that he actually killed Malware, (though he survived.) It also left him traumatized to the point where he won't even talk about Feedback in the present time.
Showdown also finally shows Malware killing two Galvanic Mechamorph guards onscreen, and the end of the same episode has Malware seemingly entering Omnicidal Maniac territory by destroying Galvan B.
Showdown Part 2 shows Malware grow bigger than even Way Big and look even more horrific. This is even more punctuated by him absorbing Way Big into himself.
The Psycholeopteren whose DNA Khyber was taking is kinda hardcore. It makes you see your fondest desire, but it is a predatory beast. Most Lotus-Eater Machine scenarios give you a long time to realize the world's wrong and marshal your Heroic Willpower, or your friends come and rescue you, or something. This thing, you've got about five seconds in la-la land before this thing eats you. And just think, aliens use this thing as a G-Rated Drug. If it's improperly contained, enjoy your Darwin Award.
Billy Billions getting trapped in Dimension 12 is guite frightening. Sure, he brought it on himself but think about it, he's trapped in a dimension where he cannot age and is hunted down by robots designed to destroy all organic life. That's scary.
And it's also scary how close he came to getting rid of Ben. Ben was too busy with the thief he caught to notice someone gunning for him. Had he not been Diamondhead at the time, who's crystalline body deflected the laser, he would have been sucked into Dimension 12 and the Ben 10 universe would have been very different.
And to throw in some Adult Fear, for five years Billy's parents didn't know where he was. For five years, they had no Idea their little boy was trapped in a dimension filled with killer robots. Truly, a parent's worst nightmare.
Store 23 was about Ben trying to find the legendary 23rd Mr. Smoothy store and lots of wacky hijinks ensue. Now, why is this episode on this page? Because Ben stumbles into a universe where 23 Ben is more of an Attention Whore and has Fantastic Racism against all aliens since Max died before Ben got his Omnitrix. As a result, 23 Ben didn't get the moral support and Character Development that would make him become the hero he was today. Wanna make it even worse? He nearly ripped this dimension's Azmuth in half!
A weird variant, but Fistina's look with her Krahoo boyfriend in Special Delivery is kinda disturbing. Even the other villains are freaked out.