This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Archie Comics' Sonic the Hedgehog
Issue 3 had everyone think Robotnik got hold of atomic bombs and went over the destruction the weapons could cause. While it turned out he had only gotten insecticide bombs, later on Robotnik did get atomic bombs.
The original Dr. Robotnik had many of these moments, such as when he gleefully tests a matter-vaporizing weapon on a pleading Overlander.
"Whoops Apocalypse"◊ from issue #51, as Sonic is plunged into a VR world where his friends have all been roboticized and turned on him. Originally, the culprit would have been Sally, who had really died during Endgame and was replaced with a robot double of her.
The reveal of Robo-Robotnik being a robot is accomplished by melting his skin off with acid.
Robo-Robotnik destroyed future!Mobius with nuclear weapons.
Bernie's roboticization◊. Her husband Jules grabs her and throws her in, and her pained expressions are horrifying.
While the plot point didn't really go anywhere, from around issue 100 to 118 Robotnik could roboticize anyone with the slightest touch, making just being in the room with him dangerous.
One Zone Wars story had Sonic accidentally kill an alternate, monstrous version of his father while retrieving half of a Chaos Emerald from him. Zonic the Zone Cop revealed himself to be an alternate Sonic, and reminded him that Jules was technically his father too.
Nack shooting Mina in the back with a realistic gun.
The fates of the original Freedom Fighters. They went off to save the king, only for Robotnik to reveal that they've been lured into a trap, which was set up by one of their own, Trey Scales (who claims that treachery is "in his nature", since he's a snake). Scales is promptly thrown into the roboticizer with his former teammates and all of them are roboticized and banished to the Zone of Silence, never to be seen or heard from again. If that weren't enough, it's later revealed by Word of God that they were eventually destroyed by Feist.
Perhaps the worst part is just why he may have done this. In the Official Encyclopedia, it's noted that he always wore the cap of the defeated Southern Baronies, who had been forcibly reintegrated into the Kingdom of Acorn after seeking independence. The same source suggests he might have sold out his partners as a final, petty form of revenge for the Baronies, placing his own patriotic pride over the survival of his species.
Robotnik's 'daughter' Mecha had laser eyes and nearly killed Sonic when she first fought him.
Eggman's Egg Grapes. Sounds like a goofy name right? Actually they're devices that suck the life from living beings and turn it into energy for Eggman to use. He ends up killing almost all of Albion's inhabitants using them.
In issue #60, the Iron Queen vowed to return after her defeat. When she finally did, she took over New Mobotropolis and Nicole.
Mina didn't take the Iron Dominion's invasion of New Mobotropolis well. Particularly Nicole being Brainwashed and Crazy.
"If you or any of your echidna-buddies cross me, you're all going up like a fireworks festival." Complete with a Slasher Smile and the green lighting, Eggman just proved he can still scare if he wants to.
Issue 256: Thanks to Eggman disrupting Sonic's Chaos Control at the end of the crossover, the entire multiverse collapsed on itself, with Mobius Prime and Blaze's world being the only confirmed survivors. Eggman has committed the single greatest act of mass-murder in the comic's history. And then Mobius breaks apart.
Sonic gets a face full of the dark energy that's seeping out of Mobius's core and, with every stressed-out moment from then on, comes dangerously close to snapping. This version of the Werehog may not be as benign as his game self.
In #262, Sonic and Rotor start drowning◊ because their air necklaces aren't fully charged, and Sonic starts to turn into the Werehog. The Off-Panel◊ is even worse about this as Sonic is his usual self... and still drowns.
In "Eggman's Dozen," Eggman shows his subordinates what he'll do to them if they rebel. He shuts off the Foreman's muscles, rendering him unable to move or talk, but can still hear and see, and locks him in a tiny, lightless box for 50 years. Sonic Universe #86 then has him change his mind, using the Foreman as the test subject for a new roboticizer instead.
Maw's ability is to inhale◊ his opponents, devouring them utterly. Where they go is never explained. Even Nephthys, one of his fellow Egg Bosses, is horrified when she sees him use this attack.
Battle Kukku XV, leader of the Battle Bird Armada, apparently has similar bomb-conjuring powers to Bean the Dynamite. When he shows off what he can do with them in Eggman's Dozen, he horrifies his fellow Egg Boss, Abyss the Squid. The panel of him about to use them, complete with one of the creepiest Slasher Smiles in the comic's history — complete with Scary Shiny Glasses to boot — is just that extra bit of overt creep to help the Fridge Horror sink in.
Scourge is just plain creepy. Having been nothing but a cheesy 80s punk in a leather jacket back when he was introduced, he seriously amped up his game — and his intimidation factor — after the long hiatus between his appearances. Sneaking into Sonic's home, he confesses as openly as the rating allows to having murdered his own father. When Sonic and friends meet Patch, the "Anti-Antoine" likewise reveals that Scourge did something to his eye to cement his new identity. By the end of the arc, hopped up on Anarchy Beryl, "Super Scourge" starts raving about how he's going to spindash both his own world and Sonic's world in half, just to prove he can, before going on to world after world, destroying everything in his wake until he finally gets the respect he feels that he deserves.
The worst part of it is, even as Scourge, he's still Sonic's Evil Twin. This is the kind of things that Sonic might do if he ever went off the deep end...
Rotor's father, Tundra, stands out even amongst the ranks of the comic's world-conquerers and mass-murderers for just how banal his evil is. He abused and tormented Rotor all his young life for wanting to live a peaceful life as an inventor, rather than a brutal barbarian like the rest of "the Herd". When Robotnik took over, rather than fight, he chose to serve Robotnik willingly and justified this as being in accordance with his Might Makes Right principles. After he was de-roboticized, he ended up voluntarily joining Eggman's forces a second time for the same reason, letting himself be Legionized in order to serve as the Egg Boss of the Artika region. And he doesn't regret what he's done at all.
Perhaps the worst part is that he's a Super Genesis Wave retcon character; in the original canon, Rotor's father was the loving Sherman Walrus, who heroically sacrificed his life fighting against Robotnik. So even without meaning to, Eggman's meddling with reality has hurt people.