J'onn's torture. It, quite frankly, looks like someone digging their fingernails inside someone's face. All bloodless, though. Even so, it's terrifying, especially when he's essentially absorbed by another Martian.
The part where he deals with the Imperium, grabbing the tentacles still embedded into his own body and dragging it into the sunlight. We see the Imperium's outer layers starting to form bubbles that quickly burst, like a hyper-skin irritation, like boils, and as it screams, J'onn delivers the line: "You live in the shadows, and shun the light. Why? Does it burn your putrid skin?"
The Justice Lords' Superman's Psychotic Smirk after he kills President Luthor, all with creepy background music.
Also, Lord!Batman asking "Do you smell something burning?" right before a cut to where we see the burned remains of the Oval Office desk and Superman standing next to it, which lets us know that, yes, he did blast Luthor.
What he says to Lord!Batman and Lord!Wonder Woman right after makes it a LOT worse. "I'm great."
Lord!Superman lobotomizes Doomsday. The matter-of-fact way in which he does it and the speed in which Doomsday goes from being relatively well-spoken to drooling are equally chilling.
In a later episode, the real Superman is actually driven by desperation to attempt the same maneuver, but due to Doomsday's Adaptive Ability, this no longer works. Thus three bits of Nightmare Fuel in one scene: 1) Superman can do that, 2) and he will if he's desperate enough, 3) and on some enemies, it still won't be enough.
Lord!Batman. The biggest nightmare in all this is that Batman himself has turned over to the dark side. That in itself is scary enough (this is the guy who sees the Justice League, all of the Justice League, as a countermeasure to himself). But what's scarier is that after Lord!Superman vaporizes Lex Luthor, all he offers is a disinterested "Well. It had to be done." He has no sadness, no revulsion towards Lord!Superman breaking one of their central tenets; in fact, he sees Superman killing Luthor as a necessary move. If Thou Shalt Not Kill was ever a principle for this version of the character, he abandoned it before even Superman.
Then there's Flash telling Lord!Superman that he couldn't kill him, since the death of his Flash was what started everything, and that even now he wouldn't go that far.
Lord!Superman: I've done a lot of things I've never thought I'd do these last two years. One more won't hurt.
Being an homage to the Cthulhu Mythos, "The Terror Beyond" is stuffed to the gills with it.
Start with Ichthultu himself, an Expy of Cthulhu, which appears as a monstrous skull-like apparition with flaming eyes and Combat Tentacles. Even worse, Hawk Girl's race use to worship the thing because it gave them technology, knowledge, and prosperity, but they eventually took a Nay-Theist approach when its exchange price of the souls of Thanagar's people became too great. Ichthultu was shown to still be bitter about the rejection.
Then, later in the episode, Flash finally turns the tables by going all out. He knocks Brainthor down, pins him, and starts tearing them apart with his fists while Brainthor screams.
Near the end of "Maid of Honor," when Vandal Savage, who was in ground zero for an asteroid hitting the Kasnian royal palace, confirms his immortality by breaking out of the rubble, still healing from the blast, resetting his bones, and screaming in a mixture of rage and indescribable pain.
What happens to the King of Kaznia, who is poisoned and paralyzed by Savage as part of his plan to take over the country. He's unable to move and is forced to watch his daughter get married to the man responsible for his predicament. Made worse, since we never see what happens to him, it's heavily implied that he most likely perished when the rail-gun was redirected to destroy the castle!
Which, if that wasn't bad enough, also means that Batman, of all people, almost killed Princess Audrey's father with a big honking space-gun! When we saw the people running out of the castle, you can see one of the soldiers carrying someone dressed in purple. The king was wearing purple pajamas. So, the king didn't actually die in the explosion. But what if the guard hadn't been on the watch?
The look of horror on Flash's face, when he briefly got spaced.
Doctor Destiny and Ace of the Royal Flush Gang are especially fun cases in this regard. Their common special ability: Mind Rape. Which is to say, they are in themselves Nightmare Fuel in episodes that use said trope as a plot point.
Joker revealing Ace's origins and her powers (she can alter your perception of reality by looking at you), while her eyes stare at you.
Then there's the scene where Ace shows the Joker that, no matter how crazy you are, there's always an even lower depth to plumb...though seeing the Joker Hoist by His Own Petard was simply priceless.
The ending where Doctor Destiny has gotten everybody but Martian Manhunter and Batman to go to sleep. They show each of the heroes going to sleep, while playing a toned-down music box in the background. Finally, you hear Doctor Destiny softly chuckling. Not an Evil Laugh, just a...chuckle. Worst of all, Superman goes to sleep and Batman calls him moments later, trying too late to warn him. End of episode.
Penny: John, please. John: You know, I never liked that name. It's so...ordinary. Especially for someone who has such big things in store. You know, a destiny. Oh, destiny! I like it: Doctor Destiny. What do you think? Penny: You're crazy. John: I think you're finally seeing the real me. (clothes turn into spooky robes) And now that I'm a doctor... (face falls off, revealing a skull) ...I think I'll perform some surgery.
Doctor Destiny looms over the Flash when he enters his dreams and delivers a chilling line.
Flash: I get it, I'm dreaming. All I have to do is close my eyes and I'll... (closes eyes, nothing happens) Doctor Destiny: Wake up?
While you're inside the dream he traps you in, you can't wake up, and the torture the victim goes through causes their heart to accelerate to dangerous levels until it eventually gives out. Batman and Martian Manhunter make every attempt they can to wake the others, and Martian Manhunter in the end resorts to entering the dreams to save the others, with nothing else working.
The cannibalistic kids in Flash's nightmare? They had nothing to do with the nightmare per se, but it was so out of nowhere... They got to be even scarier than the context of the scene. Good thing he has Super Speed. Or not.
Superman's nightmare is both horrifying and heartbreaking. It starts with him accidentally frying Lois with heat vision. We don't even see it, but from Supes' response, it must have been horrifying, especially given what we see of his reactions; of all the Leaguers, his is the most outwardly pronounced. After he accidentally kills Lois, we cut to his apartment where we see him screaming and flailing around as if in agony...and given what we see of the rest of the nightmare, it probably didn't get any better for him from there.
Green Lantern's nightmare is another one that's very effective in how relatable and relatively subtle it is. Imagine coming home, only to find that it isn't home anymore, that no one recognizes you, and that the people you care about are terrified of you for reasons you don't understand, that even your surroundings have changed.
Dee's fate at the end is creepy. He's lying in bed, seemingly catatonic and humming Frere Jacques. Who knows what he's seeing...
Even though he's on the side of good, hearing Batman's quiet humming in his head has a creepy sound to it, like you can hear him about to snap underneath from lack of sleep, and yet he's so calm...
Well, actually, that was probably him faking it, since he replaced the torturer easily enough. Shape-changing, Super Strength, phasing...he's equipped for this. Doesn't make his screaming any less creepy. Seriously, something about J'onn's voice makes any screaming, real or faked, kind of scary.
Given that the torturer looks weak when the guards find him strapped to the table, this leads to the very real question of whether some of those screams might have been from J'onn torturing him?!
Speaking of "Hereafter," there's also Savage himself in said future. There's another reason why he's become much more sedate and friendly: countless generations of living with the consequences of his actions had made him boredwith insanity and madness. Which makes the way he chirpily recalls how he killed the Justice League as if he remembering a sports game seem so unnerving.
One of the scenes in the Justice Lords episode "A Better World" has the League visit the alternate Arkham. Many villains, particularly Batman villains, are acting very much out of character. Then, you notice two small dots on all of their heads. Then, you recall what Lord!Superman did to Doomsday. Oh, and Scarface's dots are on the dummy, not on the ventriloquist.
The first person who is revealed to have been lobotomized by Lord!Superman is the Joker, who is now the secretary of Arkham Asylum. Hearing his voice and seeing his appearance to be so calm, almost serene, it really drew an unsettling feeling considering we're used to seeing him as a psychopathic, murdering clown. Who would've thought one way for the Joker to be scarier was to calm him down?
Flash's scene with Poison Ivy. Ivy's a real unpleasant, fanatical piece of work, in the DCAU and without, but seeing her like that...content, calm, friendly, and humming as she cuts the the buds off of flowers...seems just fundamentally wrong. Creepy, you might call it. Especially when you think about Ivy's obsession with plants—she nearly goes into conniptions if anyone so much as touches one of her plants. For her to go so far as to actually be "hurting" plants...it's so thoroughly not her. Even when a decapitated robot head falls right next to her, she just continues on with her work.
At the end of "For the Man Who Has Everything," Wonder Woman puts Mongul's Lotus-Eater Machine plant on him. Right before the episode ends, we get to hear painful screaming and horrible destruction, presumably all from Mongul's fantasy. And Superman wasn't the only one screaming.
This episode deserves mention for when the plant is put on Bruce: We get to relive the moment his parents were shot (in black and white, to give it a proper Film Noir feel), but in his dream, his father fights the criminal and continues to punch him. But as Wonder Woman tears off the plant, we see Bruce's father be overpowered by the criminal, zoom in on young Bruce's face turning more and more horrified as we finally hear a combination of a tearing sound and a gunshot when the plant is removed...it's truly horrifying. Made worse in that when the plant attaches to him, we see the only genuine, contented smile Batman ever has in the entirety of the Justice League run.
Even the nature of the fantasy is unnerving in and of itself. In the comic the episode was based off of, by the time the Black Mercy is pulled off of him, the fantasy had extended to growing up, settling down and having a child. In here, that's not the case. In here, his deepest, truest wish is simply to watch Thomas Wayne beat Joe Chill to a pulp. Forever.
Wonder Woman falling victim to a No-Holds-Barred Beatdown by Mongul was pretty unsettling to watch. We have seen Wonder Woman take a beating before, but this episode in particular makes it worse than the others. For instance, you had Mongul coming close to actually killing her. She had to crawl to Bruce to save him from the plant because she could hardly stand after the beating she took from Mongul. When Mongul takes her down and then stomps on her, the scream she lets out is chilling.
This episode also stresses just how dangerous Mongul is. Literally the only thing that could stop him was Superman, and he was already taken care of. Batman even states that if Superman doesn't snap out of it Mongul will kill Wonder Woman, then him, then everyone on the planet. That's right, even Batman was scared of Mongul and couldn't think of a plan to beat him other than "get Superman into the fight." Mongul himself gives a very chilling Badass Boast right before he starts beating Wonder Woman.
Mongul: You don't understand. He was the only obstacle in my way. The rest of you, are already dead.
The end of "Kid Stuff," where Mordred's spell to get rid of all grown-ups is reversed when Mordred is tricked into turning into an adult himself, and his mother Morgan Le Faye notes that the spell giving him eternal youth is now broken, leaving him only with eternal life. As if simply thinking about the ramifications of this isn't enough, the last shot of the episode shows Morgan tenderly wiping the drool from the mouth of a glassy-eyed old man.
The episode "Dark Heart". A planet being devoured piece by piece, the inhabitants mostly being able to do nothing as they see the wave of machines sweeping towards them.
In "Destroyer", Darkseid describing what he's going to do to Superman while he's writhing on the ground in pain from the Agony Matrix. Then he pulls out a Kryptonite knife and tells Superman that he's going to carve out his heart and place it on a pike as a trophy.
The portrayal of Darkseid in the DCAU is often seen as the definitive portrayal of his character (outside of comics) and for good reason: he is a terrifying character. Not just because he's the only one who can take Superman at his full power, but because he is relentlessly evil. Other villains had reasons that you could like them; at least Lex Luthor was suave, and at least The Joker had a happy attitude and comic timing. Darkseid is not that kind of villain: he is the absolute embodiment of evil.
To give a sense of how terrible Darkseid is, he is the only villain that Superman actively tries and wants to kill.
A rather small one, but the Justice League women being pitted together in "Grudge Match." Huntress and Black Canary manage to free Shayera and Vixen pretty easily, but then they find out they have to fight Wonder Woman (who could match almost Superman in terms of power). Their reactionis entirely justified. During a rather brutal fight, a few of the League girls come frighteningly close to a bloody death. Hawkgirl almost smashing Vixen's head with her mace, for example.
Also, the way Wonder Woman over-powered all four Leaguers and took absolutely everything they threw at her like it was nothing. Then there's the way she was about to kill the badly-battered Shayera and Vixen by crushing their skulls together. More terrifying is the fact that she was completely unaware of what she was doing and would never have remembered it had she been able to follow through.
The vision the Question sees while being TORTURED in "Question Authority" is pretty chilling.
The Question being tortured period was chilling.
He was missing for almost a week before Huntress tried to get Superman's help. Even then, nobody in the League noticed that he was missing.
Static's howl after getting sucked into a spatial rip was rather chilling, as was Terry's death by the Dee-Dees. More chilling was the fact that the universe was collapsing all around them and they were all completely helpless to stop it.
The whole thing is practically a Kill 'em All episode: Wonder Woman fades out of existence thanks to Chronos' meddling with the timestream, one of the bad guy's own henchmen is dropped in the Cretaceous to be killed by the mass extinction that wiped out the dinosaurs, Terry is ripped limb from limb, and—as mentioned before—Static fell through a tear in the space-time continuum, plus the implication that every other member of the Justice League is already dead. Green Lantern nearly had something like this happen to him, too—luckily for John, he was just temporarily replaced by Hal Jordan and came back after a few minutes.
Batman trapping David and Enid in a time loop to ensure that David never enacts the chain of events that occurred over the episode. That is one chilling And I Must Scream fate.
It's easy to forget exactly how powerful the Martian Manhunter is, since he spends so much time being The Aloner. Then Task Force X sneaks into the Watchtower, makes off with the secret weapon they've been sent for, mops the floor with several unexpected obstacles, and suddenly comes face-to-face with That One Boss: J'onn. And suddenly he's really creepy.
In "Flashpoint," Lex Luthor hijacks the Watchtower's Binary Fusion Generator, forcing it to fire on an abandoned Cadmus facility. When the gun goes off, the scene cuts to a peaceful suburban neighborhood...that suddenly goes very quiet as the sky starts to light up. Then the blast wave comes and nearly levels the city, followed by a mushroom cloud. Aside from the fact that, somehow, nobody (onscreen) is killed, and there's no residual radiation, the entire sequence is frighteningly reminiscent of a nuclear attack.
That's right, kids! Death from above, with no warning, no escape, and no explanation! It could happen to you before you finish reading TV Tropes!
The ending of "Hearts and Minds." Despero's army is turned into trees, all the while they are aware of this. Their faces as this happens tells everything you need to know. Especially chilling one a close-up of a face with face stuck in a scream, while only one eye is left open...
The scene in which Despero tries to Mind Rape Hawkgirl which causes her to scream in agonizing pain that grows louder and more intense which is pretty terrifying until Green Lantern saves her.
Galatea's Family-Unfriendly Death (Supergirl frying her with the reactor), as well as a good shot of her twitching corpse!
As a clone of Supergirl, she might have survived. Still disturbing, though.
Seeing Amazo tear through the Justice League to get to Luthor. In space, he destroyed a fleet of Javelins and defeats nearly dozens of heroes including Green Lantern, Dr. Light, Captain Atom, and Superman himself. In the sky, he goes through the second wave (Supergirl, Fire, Red Tornado, and Rocket Red) like tissue, during which he splits Red Tornado in half and destroys him. He doesn't even try in the last wave (Wonder Woman, Flash, Steel, and Ice). The thought of something that powerful existing is horrifying. Dr. Fate was not kidding when he claimed Lex was saving the world.
J'onn is a master of subtle Nightmare Fuel in this series. Take his mental interrogation of Kragger, one of the Thanagarians; he couldn't normally read their minds due to mental defenses.
And then in "Hunter's Moon," we see the consequences of this interrogation. Kragger is now a babbling fool who has been Driven to Madness by J'onn.
He gets a great one during the series premiere, tricking a pair of Imperium soldiers into cornering a few League members so he can get the drop on them from behind. He puts an intangible fist through each of their chests and goes solid. Ouch. Lampshaded by the Flash who highlights how J'onn veers into being a straight up Horrifying Hero because of this.
Flash: Is it just me or does he creep you out too?
While generally amusing, the entirety of "Legends" has some extremely creepy subtext; indeed, the fact that the world is so bright and sunny makes it all the more frightening when you put together the pieces. The ideal, idyllic 50's comic book fantasy world was created by a young child who had to experience his entire world go up in flames when a nuclear war broke out, was mutated by the fallout into some...inhuman...cancerous...thing, and was driven so insane that the only he could cope was by using his newfound psychic powers to create an eternal happy dream world where none of this ever happened.
The Reveal of the real world is chilling when you consider how close our world has come to that and that it could still end up as such.
Tala's screams as she's being used up in Luthor's attempt to revive Brainiac in "Alive!" (The show-runners even admitted they were unsettled by this, even after having toned it down considerably from the original recordings.)
Immediately before this, when Tala begs Lex to spare her for betraying him to Grodd, she tells him she's "a sick person." When she realizes he planned on using her up even before she betrayed him, he coldly replies, "I'm a sick person, too."
And she ends up releasing Darkseid, endangering Earth, just to screw Lex out of possessing Brainiac and for spurning her.
Grodd getting spaced in this episode was pretty disturbing, as well.
Also from that episode, Killer Frost kills half of the Legion of Doom, ON SCREEN. Just to get back in Luthor's favor.
Okay, she doesn't KILL them per say, but we know they're finished.
There is a (relatively) minor one in "Eclipsed" with the soldier who is possessed at the beginning: this guy wakes up and learns that he killed his whole unit, with whom he seemed rather close. Especially since the last time we see him in the episode he's still held responsible for it.
The song people possessed by the Dark Heart sing starts out kinda narmy until everyone but Flash gets possessed and starts singing it. Combined with the dark, enclosed watchtower with no exits...really hammers home the oppressive nature.
The nerd who performed the satanic ritual in "Wake the Dead" definitely got killed by Solomon Grundy.
The scene in "Epilogue" involving eight-year-old Terry and his parents walking from a movie and as they start to head home, the Phantasm begins stalking them from behind. Upon getting closer, she raises her hook hand, moments away from killing Terry's mom and dad, all to give Terry the motivation he needed to become the next Batman. Even more Nightmare Fuel when you learn that the Phantasm was ordered to kill Terry's parents so Terry could experience the same pain that Bruce did so he'd take up the mantle and was real close to doing so.
Also a rare case of Even Evil Has Standards being invoked to avert Nightmare Fuel. The Phantasm is willing to murder unsuspecting strangers but, when it comes right down to it, can't bring herself to traumatize an eight-year-old for life.
Amanda Waller, bad enough she proved she knew Batman's secret identity the first time they met. But every single time she talks about the clones or mutated soldiers Cadmus created, she's always got one of the nastiest, evil grins ever seen. They're weapons for deployment, nothing more.
When Green Arrow tries to call out Superman in 'Flashpoint" on seriously considering burning a government agency to the ground and generally putting himself and the team above humanity as of late, all the attention Superman can spare for him is to say is that he could care less about his opinion, or that Batman recruited him to be the team conscience. When Arrow admits that he's starting to become scared of Superman himself it's pretty understandable, especially since if Superman had just snapped then and there he could have blown Queen's brains out with the flick of a finger for talking back to him, or simply turned him to ash with a glance - not an unreasonable response from Lord!Superman, who Superman teeters on the verge of becoming for the entire Cadmus arc.
"Panic in the Sky." Just...just "Panic in the Sky." The League just lost control of their Kill Sat superweapon that they save for emergencies like the events of "Dark Heart," which they fear may have killed hundreds if not thousands of civilians. Understandably, the President is pissed about this and the founding members of the League, sans Batman, decide to submit to government custody until they can sort it out. While they're gone and the Watchtower is still out of commission, Cadmus sends Galatea and an army of Ultimen to attack the Watchtower and kill—not arrest, not defeat, KILL—every last person on the Watchtower. That includes the non-powered civilians who run the Watchtower's everyday systems. In particular, we're treated to a group of those non-metahumans hiding in a safe room when one of the Shifter clones rips the door open, then transforms into a Tyrannosaurus rex. The workers are clearly ready to fight for their lives as they charge at her and the Ultimen are eventually defeated, but one shudders to think about what probably happened to them.