Ogremon in "Home Away From Home," pictured on the right. Those eyes.
Raremon could easily come off as this. If Mr.Face raped a bionic manatee, this would be the result.
Myotismon in general. Venom Myotismon is even more due to his...eating habits...
Gatomon's life under Myotismon qualifies, and Wizardmon getting shredded by Myotismon, even in the edited version
Piedmon's, ah, "key-chain hobby." What makes it even scarier is his hunting them down one by one in a methodical and sadistic manner. Except for the fact he doesn't actually kill them, it's almost like watching a slasher killer hunting down his victims one by one.
Machinedramon. The combination of his Creepy Monotone and the fact most of his dialog is composed of how much he enjoys killing people makes him one of the scariest villains in the show.
Machinedramon: Just what I was looking for, victims!
The penultimate episode, when Apocalymon pretty much deleted the Digidestined and their partners. That's got to be pretty traumatizing for a kid watching the show...
The trailer for the PSP video game adaptation. At first it's all bright and cheery and gives you a real nostalgia kick. Then the shot of the logo lasts a bit too long and starts to glitch...the camera pulls back to reveal the background of the Internet from Our War Game! all in complete silence. Then you hear Diaboromon giggle. Unnerving stuff.
Dark Lizardmon's fate: It was captured by Hypnos, interrogated under torture and literally torn apart for analysis while fully conscious after Yamaki was done, in a process that actually looks more painful than the equivalent, that is to say an autopsy on a living human. Not to mention that this is a close up to what Shaggai/Juggernaut does to it's victims in episode 14.
An early warning of things to come, episode 14, where the dying screams of the Digimon deleted by Shaggai/Juggernaut can be heard. A tamer version of Homeworld cataclysm's corruption by the beast.
Everything that happened to Juri after Leomon died is pretty creepy. So much so that Juri in general might just become Nightmare Fuel for people upon re-watching the series now that they know everything about her.
Her creepy hand-puppet might have already been this.
In episode 47, the Mind Rape sequence of her reliving witnessing her mother's death. And the fact that this goes on for weeks.
As scary as Dark Evolutions are, Megidramon definitely takes the cake. It certainly doesn't help that its name is derived from the words "Megiddo" and "Dragon", considering that Har Megiddo is the mountain, where the apocalypse is (according to the bible) going to start. Har Megiddo has later been given its more popular name, "Armageddon". In other words, Megidramon's name is closer to original idea of the end of the world than "Armageddon". It doesn't help that before it Takato is practically SCREAMING about how he is going to make Beelzemon suffer For killing Leomon.
The Body Horror Beelzemon undergoes after absorbing Taomon and Rapidmon's data. It involved Beelzemon's shoulders bulging until parts of Taomon and Rapidmon started protruding out of his skin with Beelzemon clearly in pain from the experience. Surprisingly enough, Saban kept this part intact, completely unedited.
Mephistomon dropping his human disguise in Battle of Adventurers, specifically the part where his human head retracts and his normal one bursts out.
Duskmon, and not just for his appearance either.
"YOU MUST CHOOSE TO FOLLOW ME OR BE DESTROYED" or "Follow me or die. Which will you choose?" And then in big Japanese font just the word "Choose." at the end of Episode 49 in the English dub and subbed versions. And for more chills, think about it: every screen in Shibuya and probably the rest of the world says one of those messages depending on the version...AND THEN YOUR TV SAYS IT AT THE END.Lucemon is warning YOU, THE VIEWER. They make you believe for a second that Lucemon has entered OUR WORLD AND IS TAKING IT OVER WITH ABSOLUTELY NO EFFORT. It gets worse when in the dub, HE ACTUALLY SAYS IT. And in the voice of what sounds like Terriormon from Tamers with a slit throat!
Digimon Savers/Data Squad
The Gizmon. They already look wrong, but then you see what they do. They're designed to kill Digimon. Not defeat, or capture, kill. And any Digimon they kill stays dead, without turning into a egg. And they rampaged across the Digital Worlds ten years before the series begins, massacring its population.
Also, the shot of Digimon in a lab, hanging in tubes. The implications are all kinds of wrong, especially since many of those Digimon are In-training level.
Digimon Xros Wars/Fusion
After having absorbed the Gehenna Sphere, Lucemon.
The Young Hunters Leaping Through Time
The state of Blossomon's victims after he drains them in episode four. Seriously.
This may be intentional or not, but Dracumon's evolution to Yaksamon shows him ripping his own face off.
Sephirotmon was just plain creepy. The scene where laughing children appeared from inside his mouth didn't help.
Digimon: The Movie
In Digimon Adventure, when Koromon decides to give his human friends a face hug. Anyone who seen Alien would find this horrifying.
The X-Antibody in its own right is not so bad. What's worse is the Death-X-Antibody. If you have seen a Doru-Greymon, you do not want to see a Death-X-Doru-Greymon. It's essentially the same, only darker, more diabolic and with claws that can pretty much rip anything apart.
X-Evolution has the probably most evil Digimon ever shown: Death-X-Mon (or Dexmon, depending on translation). It isn't so bad that it looks like a mechanical dragon, combined with a demon of some sort. It is immortal as long as the main character, Dorumon, is alive. The solution: Dorumon, Digivolved into Alphamon, summons the Ouryuuken (Ultimate Warblade Dragon King Sword, in itself another digimon but that bit isn't mentioned in the film) and throws it like a boomerang, so it hits himself, Death-X-Mon and Yggdrasil, which is the only thing keeping the world from being destroyed.
Somewhat better, somewhat worse: Afterwards, Omegamon takes Dorumon's Digicore and becomes Omegamon-X, and uses a brand new technique, called "ALL DELETE!", which finishes off Yggdrasil leading to the reboot of the Digital World, without Yggdrasil or the Death-X digimon.
The Royal Knights (the good guys) work for Yggdrasil (the deity) who created Death-X-Digimon, including the Death-X-mon mentioned above (The Dragon). And at first they never question a command.
Any battle involving Omegamon. His destructive power is far above anyone else's. In one scene, he managed to curb stomp MetalGarurumon-X and WarGreymon-X, following that with killing Dukemon note that Dukemon let himself be impaled, because "There was something I wanted to check". And that's despite Dukemon being on Omegamon's side.
The opening scene. We get to see Leomon dying in front of Dorumon... and this scene is shown again and again whether it's necessary or not.
Most of all, the deaths of the surviving digimon. Ways to die include death by virus (collapsing and dissolving), disintegration by energy beam, impaling, literally crushing the skull, being ripped to shreds and eaten alive, to list the most memorable ones. All shown onscreen, while the last two where preceded by the endless bloodthirsty cries of the swarm of Death-X-DoruGreymon. That probably had to do with why the film was never dubbed.
The Seven Great Demon Lords in general. A group of uber-power demons who do whatever they like with near impunity, with control over every Digimon in the Nightmare Soldier family, which acts as their army. And if a Digimon is killed by one of them, rather than being reborn as a Digiegg somewhere, they become a part of said Demon Lord.
The profiles on the early (pre-2002) cyborg Digimon, which imply someone or something was using them as guinea pigs to create Mugendramon and Chimarimon, and given what those two Jogress into... yeah.
Speaking of what they Jogress into, Millenniummon is pretty damned creepy. A near-unstoppable monster that's every bit as insane and evil as they are, capable of forcing its enemies into another dimension when it fights them. And it gets worse. Kill a Millenniummon? Its spirit will be reborn as MoonMillenniummon, which doesn't have a body and can't be killed, while its body just gets right back up again, even more powerful than before and capable of travelling through time. And just for added fun, ZeedMillenniummon is an Omnicidal Maniac.
Megidramon manages to get even more terrifying than Tamers already made it. Its body is made of Chrome Digizoid, meaning it's near-completely indestructible. Near-indestructible, insanely violent and capable of breaking reality just by existing.
And apparently Megidramon is capable of Voluntary Shapeshifting to ChaosDukemon. The one good thing about Megidramon was that it was apparently just a mindless beast. Now imagine something born ferociously violent, indestructible, capable of breaking reality by existing, and it's intelligent.
Chaosmon are really disturbing, even by the standards the Digital World has. They're not supposed to exist, which shows by the very edges of their bodies glitch. Even worse, the Digimon that wind up creating a Chaosmon are still alive and conscious in its shoulders, with their severed heads turned into weapons, in a dark twist on Omegamon's design.
Remember SkullGreymon? And remember that bone club Orgemon carries around? That's a SkullGreymon's femur. How the heck did an Orgemon get its hands on a SkullGreymon's femur.
Diablomon (Or Diaboromon, if you prefer your dub names) is already creepy, but the purpose of every Diablomon ever? Hack into human military banks, and destroy humanity with nukes.