This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Batman: The Animated Series
That mortifying moment in the opening credits when a massive thing made of the very shadows itself swoops in front of the fleeing bank robbers, and narrows its eyes in cold Tranquil Fury.... we the audience get to feel the sheer horror racing through the hearts of criminals who come face to face with the mystical figure of Batman.
Made worse by Batman's gargoyle like profile silhouetted by a roaring flash of lightning.... shiver.
Clayface is certainly a terrifying character already. His introductory episode was bad enough, but there's a follow-up episode that had him creating a little girl out of his substance to act as a "lookout" to see if it was safe for him to come out of hiding. She acquires a self-identity and tries to escape and befriend Robin. Nevertheless Clayface reabsorbs her, to her terror.
"Feat of Clay". It all starts with a man being held down as you see chemicals poured on his face, while he thrashes, screaming. It gets more fun when you see him rip chunks off his face to throw at people, and watch him mutate in all sorts of demonic shapes. Oh the nightmares.
NOTHING says "Don't Do Drugs" like seeing Mr. Hagan forcibly overdosed and left in the backseat of a car in the back alley. He starts to melt.
At one point, he infiltrates a Renuyu infomercial taping as an old woman, exposing everything the company's hidden about the product. When he reaches the last line - "Why don't you tell them... about me!" - he warps into Clayface. The sudden vocal shift makes it particularly scarring.
How about his first "death"? When Batman tried to reach out to Clayface by showing him all the people he was when he was human, Clayface starts horrifically morphing into each and every one of them, including Bruce Wayne, before accidentally electrocuting himself trying to break the TVs. JESUS.
And then there's the end, when Batman realizes that Clayface faked his death. The very last shot of the episode has Clayface disguised as a woman, laughing at how he's fooled everyone... and while still in disguise, "her" eyes transform into his yellow pupiless ones. It's creepy.
In "Mudslide" Clayface pulls Batman inside his body in order to smother him to death. Batman is seen struggling to get out (at one point a clay-covered silhouette is visible), and Clayface spends the whole time describing how his struggles are getting fainter and his heartbeat is growing weaker.
Clayface's whole terminal illness, in which he's slowly melting, is very disturbing, especially since it ends with his apparent death.
One word: ManBat.
The scene where Langstrom, creepily calm, explains that he's addicted to the Man Bat formula and then transforms right in front of Bats. The episodes Animation Bump doesn't really make things less nightmarrific.
There is a followup episode where someone has managed to duplicate the ManBat formula, and all clues point to the reformed Dr. Langstrom. Fridge Horror kicks in as you realize Kirk truly has reformed and is starting to wonder if he is simply unaware of his Enemy Within. Even worse, it turns out the new ManBat is his wife, who had absorbed some of the formula through a wound she had while she helped him destroy the formula. That episode launched Kirk straight into Woobie territory.
And then there's his wife's transformation in that episode. Her screams that grow more inhuman as it goes on aren't only terrifying in their own right, but also give a hint as to how painful the transformation must be.
Anything to do with Scarecrow. (Except for the episode that introduced him, which had bad animation and gave him a very un-creepy booming voice.) As befitting his name, he is terror incarnate, exposing people to their greatest fears which end up terrifying the audience as well. His image-upgrade in The New Adventures of Batman from a skinny dude with a stupid mask to a corpse with a rope around its neck certainly doesn't help matters. Nor did getting Jeffrey Combs to do the voice work.
"Never Fear". When Bats discovers Scarecrow is giving people chemicals that makes them dangerously fearless (the opposite of his usual MO), he starts snooping and gets himself captured. He excuses his actions by pretending to be a common thief - which doesn't stop Scarecrow from giving him a dose of the stuff, causing him to jump into the water with a mess of crocodiles. They pounce, he goes under, and we see a huge cloud of blood swirling up through the water as Scarecrow walks away smugly... Guess who was actually bleeding, though.
The scene in the Scarecrow's first episode, "Nothing to Fear", when he gasses the dean of Gotham University, who then looks at his hands and sees nothing but their bone structure.
"Dreams in Darkness". Batman's nightmares. The first one involved the death of his parents and it ended with a giant gun pointing at Batman as he was surrounded by flames. In the second one, the Joker appears and turns into another villain, who then turns into another villain and so on (Joker -> Penguin -> Two-Face -> Ivy). Batman then gets pulled into an abyss where he's devoured by a giant Scarecrow. The worst thing is that in the second dream, both Robin and Alfred watch the whole thing while saying that it's for his best.
The Scarecrow is unnerving at best, but there's one particular shot of him in the episode "Fear of Victory", seen through the eyes of a Mook dosed with his fear chemical, that looks like all your childhood nightmares condensed into one snarling visage. When next we see the mook, he's curled up under a prison cot, unable to do more than shiver.
The Scarecrow himself was actually kind of cartoony during his first incarnation in TAS, but his redesign when it became part of The New Batman/Superman Adventures is bone-chilling. The fact he's voiced by Jeffrey "Dr. Herbert West" Combs, that just goes beyond the pale.
His first redesign, with that snaggle-toothed grin and those unblinking eyes bulging out of the black holes of the mask, isn't that pleasant to look at either, especially when enhanced by the fear toxin.
The scene where Batman is walking through Arkham Asylum to Scarecrow's cell, and passing Joker, Ivy and Two Face on the way, sitting in their bare cells, submerged in their own little worlds. Joker and Two Face don't even look up when Batman passes, Joker playing with a deck of cards and Two Face staring at his coin. Then there's Joker's laugh when Batman notices that the Scarecrow in the cell is a fake. Did he know the whole time?
The episode "House and Garden" features Poison Ivy with a husband a kids that turn out to be plant-based clones she created. We find this out when several pods in her basement hatch babies, who, while calling for "Mommy" grow into hideous monsters in a few seconds. Sadly, this was closest Pamela could get to being normal. No wonder she got so bitter later on. (See below)
They top this with a later episode, "Chemistry," in which a man is revealed to be one of Ivy's creations when she rips off his skin. Later, Robin sprays the plant-guy with defoliant, which causes him to melt slowly and graphically, including his eyeballs falling out and floating off. Bruce's new wife turns out to be another plant-person when her legs turn into vines... and the last we see of her is her face staring out of the porthole of a sinking ship as Batman flies away.
"Eternal Youth". Ivy turns people into trees and says that the initial layer is just an exoskeleton and it would take months for them to fully transform. The figures themselves, including and especially Alfred, are nightmare-inducing in their own right.
Ra's al Ghul's Psychotic reaction after being put into the Lazarus pit, and nearly throwing his own daughter into the pit!
The end of "Showdown". In this episode, Ra's Al Ghul and his League of Assassins kidnap a resident from a Gotham rest home, and leave a tape for Batman, on which Ra's Al Ghul relates a story about how in 1883, his plan to take over America was thwarted by none other than Jonah Hex, who was seeking to claim the reward for Ra's' lieutenant, Arkady Duvall. In the end, Hex captures Duvall and turns him over to the authorities. After this story concludes, Batman and Robin catch up with Ra's and his still-unknown captive... who turns out to be an impossibly aged and senile Duvall. Ra's explains that Duvall is his son, that his longevity is due to bathing in the Lazarus Pit as a young man, and that his mind was completely shattered by his 50-year sentence of hard labour. Even though Duvall was cruel, arrogant, and completely loathsome in the flashback, that's still pretty rough, especially when you consider the chances of many of us in this day and age living to extreme old age and ending up like Duvall can't be ignored, and that it's already happening/has happened to many people.
That such sentences really are handed out in real life is disturbing itself - they are 'worse' than a life sentence, as Ra's explained: "Nobody expected he would complete those years". For someone with an extended lifespan, they're probably worse than execution.
"See No Evil". A psychotic man used an invisibility suit to secretly trick his daughter to leave with him. The man in question was an ex-con whose wife had divorced him, and judging by the restraining order and her violent reaction to his company, he was most likely abusive. He becomes invisible in order to pose as his daughter's imaginary friend, steals expensive jewelry for her, and finally attempts to kidnap her - but is then exposed. Bats intervenes, and the episode ends with the little girl telling him that she and her mother are going to move away, "somewhere Daddy will never find us" - it's not just scary, it's a Tear Jerker.
Parents watching the show might start to get chills as early as his first visit, where the girl's "imaginary friend" picks up her toy and starts luring her to the open window.
It's even worse than that, as an adult. As a kid, you have an idea of why Lloyd taking his daughter is bad; because he's a criminal, and she'll never see her mother again. As an adult though, when you see how obsessed he is with her, you start to getthe full picture...
In "Moon of the Wolf" the thought of Romulus presumed to be trapped as a mindless Wolf Man because he was prevented from getting the antidote because Professor Milo dropped the antidote when werewolf-Romulus got all snarly at him.
This is lessened slightly if you've read the Neil Adams comic Moon Of the Wolf was based on. Romulus moves to Alaska where he makes a living as a hunter and trapper, except three days out of the month, when his wolf form runs with the wolf packs
A brief segment of "Moon of the Wolf", ending with the mad scientist threatening the guy with, "If you want the antidote, you're going to do everything I say."
Anthony Romulus: You fool! There's not telling what the werewolf might do!
Maybe he commanded her to go to another room and change? For all his faults, Tetch's attraction toward Alice had a Courtly Love feel to it.
The episode with the Sewer King and his underground child slaves. Thankfully, Batman took him down; in fact, Batman was so enraged that he was trying to prevent himself from crippling the guy on the spot - or worse - and made the Sewer King acutely aware of that.
The storyboard subtitle for this scene was "BANE IS PISSED!"
A bit more subtle one with Charlie Collins, the poor guy who inadvertently insulted Joker for cutting him off in traffic. He kept changing his name and moving, but the Joker never lost him, blackmailing him to do his dirty work.
In particular, the moment when Charlie is yelling at him in traffic and the Joker slowly turns and just grins at him, followed by the calm, easy way the Joker starts following him is the stuff of nightmares.
The plight of Charlies Collins in this episode is almost Kafka-esque in how surreally terrifying it is. Imagine driving home one day only to get into a random road rage incident with the most infamous, dangerous and readily identifiable psychopath quite possibly on the planet. That's the kind of misfortune that could get you to thinking the universe is out to get you...
In the same episode, Joker sprays Gordon's honor ceremony with a paralysis gas, then pins a timebomb to his tuxedo. Everyone gets to watch the clock tick down while being able to nothing about it.
The poor schmuck who thought he killed Batman was thrown into a coffin by the Joker and being lowered into a vat of acid.
Anything with Joker is horrifying, from disguising himself as a harmless party magician so he can kidnap the mayor's son to the creepy, horrid smiles his victims wear.
Especially the first time they show the effects of Joker Venom in The Laughing Fish. Not only does the poor guy have what's best described as a laughter induced seizure, but his eyes bug out to about twice their normal size and his mouth twists into a horribly wide rictus as the unwilling laughter gets more and more terrifying.
It's especially bad when you consider what the Joker Venom represents. The writers were told that they couldn't just kill people on a children's show. Something about traumatizing youths. Anyway, the writers decided that, instead of just shooting/stabbing/blowing up/drowning people, as he usually does, The Joker would attack them with a sort of nerve gas that made them laugh uncontrollably (and ostensibly painfully), and then freeze in to a wide grin. Frankly, since I was a kid, I always assumed that anyone who was afflicted by the Joker Venom that we didn't see alive later, or at least hear about surviving, DIED. Otherwise, the Joker Venom wouldn't be so big of a deal. You'd get hit with it, take an antidote, and move on. But when you think of it as similar to, say, Mustard Gas (not in overall effect, but in lethality), then it gets a bit more serious. Thusly, The Joker maintains a staggeringly ridiculous body count.
The more you think about it, the more Paranoia Fuel this situation generates. To give a bit of background: The Joker attacked the guy in the first place because he explained that Joker's Joker Venom-afflicted fish (creepy in their own right) couldn't secure a copyright. Such logic works on Joker as well as you think it would. The guy even explained to Batman that it wasn't even his fault that Joker couldn't get a copyright; he was an ordinary pencil pusher. And Joker still comes after him. In the words of the comic that the episode was adapted from: fail to conform to The Joker's mad logic, and you've just dug your own grave.
It gets worse. The Joker had Harley spray Francis with the first part of the gas before Francis actually refused Joker's request for a copyright. The Joker KNEW he couldn't get a copyright for the fish, and he just wanted to kill off the pencil-pushers anyway.
In "Batman: Mask Of The Phantasm", A man DIES OF LAUGHTER!!!
In Mask of the Phantasm, the corpse of the mob boss the Joker killed.
"Beware, The Creeper" is mostly funny, but the scene where the Joker has attacked Jack Ryder with the Joker Venom, causing him to fall helplessly to his knees while pleading "help me!" in between horrible forced laughter is terrifying.
In the same episode of "Beware the Creeper". It may not be much but Joker's paranoia and weirded out fear of the Creeper is understandable. Think in Joker's position for a moment. You're trying your hardest, concentrating on your favorite past time of taking on the Bat. When, surprise! Surprise! You tangle with someone or something that barely looks human. Crouched down, lurking, nearly invincible and persistent and zanier than yourself! It may be played for laughs but seeing the Joker actually cringe in uncomfortable fear and actually call someone else (besides himself of all things) a lunatic is a bit jarring.
As mentioned above, the Joker goes to the mayor's house disguised as a party clown. However, he doesn't go to kidnap the mayor's son. His original intent was to blow the garden up with dynamite, along with the mayor's social circle and the children attending his son's birthday party.
And then there's the time he had a creepy robot clown driving his boat that emitted a cloud of laughing gas all over Gotham. It seemed pretty innocent until it was established that lengthy exposure to said gas would result in untreatable insanity. Which really hits home when we see Alfred—- Bruce's surrogate father—- afflicted by the gas.
The episode "Mad Love" is this. Pratically because of the abusive relationship between Joker and Harley. It stands out as being a Truthin Television made episode since there are actual people like that out there that abuse their loved ones. It can also count with some Tear Jerker thrown into it some too.
The first time, the Joker's line "You have WHO tied up WHERE?!" is pretty funny...but watching it again and seeing the rage in Joker's eyes? Brrr...
The Hand of Fate in Riddler's introductory episode was inexplicably frightening.
A giant disembodied hand that will randomly whisk you off into the sky if you make the slightest mistake? While you're on a sadistically short time limit? To a kid who's watching this? Yeah. Freaky.
What about his first appearance in the episode "If You're So Smart, Why Aren't You Rich?" It's oddly animated compared to the rest of the episode, which gives it an unnerving Uncanny Valley effect.
Batgirl's dream sequence death was particularly traumatizing, as she falls from a high rise, onto her father's car. Made even worse by a censorship edit that put the camera inside the car with Jim Gordon as his daughter hits his hood.
Batman's implied change of policy in this episode.
Bane: "A fight to the death?"
Batman: "It makes no difference now."
"Avatar". The immortal Egyptian queen, who at first looks beautiful to Ra's, then turns out to actually look... well, like a bazillion-year-old mummy woman should.
Two-Face. He starts off seeming like a normal nice guy, then his second personality takes over and he spends the rest of the series chaotically basing his every decision on coin flips. Then there's the burn scars, which are somehow a thousand times scarier because they aren't realistic. They took artistic liberties and made them sky blue, swelled up his lips on one side and made them hang open, and gave him that freakishly enlarged, yellow, blind eye.
When Harvey Dent saw what happened to his face. His poor girlfriend wasn't the only one who screamed.
The ending of Judgement Day, with Harvey in his prison cell, playing out a trial in his own mind:
"How do you plead?" "Guilty... guilty... guilty..."
In the origin episode of Two-Face, Rupert Thorne is trying to blackmail Harvey Dent (with the information of his split personality, pre-accident) into looking the other way, and offers him a trade. Harvey is getting visibly more and more pissed as Thorne details the trade, and then suddenly goes completely calm. "There's just one problem." And then his face turns to sadistic evil incarnate and in his creepy, psychotic criminal Two Face voice says, "You're talking to the wrong Harvey." He then proceeds to kick the crap out of Thorne and his goons. It's not creepy due to gore or torture, but the sudden switch from Harvey Dent to "Big Bad Harv", and the lighting and way his face contorts, is 100% pure grade A horror to younger viewers.
Before that, when the therapist is trying to reach the Two-Face alter:
Also during the scene with the therapist, when she's attempting to talk to him at one point lightning strikes, and the flash that appears over his face is the scarred Two-Face side. It lasts only a split-second, but it's enough to get burned into the viewer's mind and get a good subliminal scare.
Before Bruce learns that Harvey has been seeking help for severe anger problems, he jokes to Harvey that if Harvey didn't marry Grace (his fiance) soon, he'd maybe just steal her away. A few minutes later, Harvey gets the bad news that the judge has thrown out a case that Harvey had spent months preparing. Harvey gets angry and Bruce, like any good friend, goes to ask him what's wrong. Harvey turns on Bruce and Grace has to stop him. That implies that Big Bad Harv didn't think Bruce wasn't joking when he made that comment earlier. Seeing how he reacted when a criminal made fun of him earlier in the episode, what would Harvey had done had Grace not been there?
When he had the plastic surgery in "Second Chance" to get his face repaired. There's a brief moment where it seems he's going to go under the knife on camera.
In "The Demon Within", Jason Blood says that Klarion turned his parents into mice, and then we get a close-up on his snarling pet cat. Nothing is stated outright; the audience are left to draw their own conclusions.
One shouldn't watch Mask of the PhantasmandReturn of the Joker together. For the first time. Right before bed. You'll have nightmares about being stalked and chased by the Joker.
Mr. Freeze has such moments. There's the title card for "Deep Freeze" wherein a mostly silhouetted Mr. Freeze ominously stares right at you with the piercing red glow of his goggles.
"Cold Comfort" is a pretty disturbing episode in itself. After being accustomed to Mr. Freeze as an Anti-Villain who just wants to see his wife healthy and alive again, he's become even more emotionless and cruel, in addition to being hellbent on destroying everything Gothamites hold dear just because he can no longer be happy. And then there's the revelation that his condition has destroyed most of his body, rendering himself just as a living head in a robotic suit. Not to mention when Batman tries to ambush Mr. Freeze as he pilots his craft, only for the latter to suddenly whirl his head 180 degrees onto him with an enraged glare.
Such is the power of B:TAS's horror that it extends to the damn activity center based off of it. Never mind the creepy ambiance. Never mind that all the games set in Gotham pit you against such pleasant fellows as Two-Face and the Joker (the game set in the sewers implies that Killer Croc is there, making it even worse). Never mind that all that can be heard in Wayne Manor is that damn clock. If you try to continue a game, you'll first have to confirm whether or not you actually continue it or start a new game—on a blood-red screen of the Joker staring right at you, taunting you with the knowledge that whichever choice you make, you'll never catch him. Oh, and every time you exit back to Gotham, both he and Two-Face laugh at you from off-screen.
"Heart of Steel"! To count the ways: HARDAC is a rampant AI born of a desire to make it so that accidents do not happen. Its plan is to "replace" humanity with robots. To this end, he starts by replacing key figures in Gotham, like Gordon and the Mayor... the robots, when threatened can move in positively insectine ways, and while the animators may have wanted to make their movements inhuman to illustrate the fact, their success means we have horror on the screen. All that, plus, the interesting little scene where Batman and Barbara collectively hurl Harvey Bullock into the bat signal.... thankfully, it was a robot replacement, but for all they knew, that was the real Harvey Bullock and they just killed him.
The follow-up episode "His Silicon Soul" introduces the Batman duplicate isn't anymore pleasant.
On the subject of the duplicate, at the beginning of the episode, we have no idea at all that it's a duplicate right up until a mook shoots it, only for said mook to get an "Oh Crap!" moment upon seeing a hole full of circuitry in its stomach. And later, when the real Batman shows up, the mook, traumatized from his encounter with the duplicate, exclaims, "Keep him away, man! He ain't human! Get it away from me!" And then after Alfred also discovers that the Batman is a duplicate, he escapes into the Bat Cave and activates the knockout gas. Then it appears right behind Alfred, unaffected by the gas, and takes off the gas mask Alfred is wearing, forcing Alfred to breathe in the gas, which knocks him out.
The episode "Baby Doll" revolves around a washed-up actress with dwarfism who takes revenge on her former castmates. She continually switches off between the child voice she did on the show and her real, "adult" voice. This continues to be creepy throughout the entire show until the climax in a hall of mirrors at a carnival, where she sees herself in a funhouse mirror showing what she probably would have looked like as an adult without the condition. She then rages at the Dark Knight for foiling her plan, shouting, "Why couldn't you just let me make believe!?" before breaking down and crying. It perhaps goes without saying that this was an episode written by Paul Dini.
This is a great example of a creepy episode that also ended up being a tear-jerker episode, as mentioned above. The last time the actress says, "I didn't mean to!" is just so tragic; no matter what she just did over the last 20 minutes, it's hard not to feel sorry for her just then.
Any episode that had the Ventriloquist and Scarface. Not outright terrifying, but subtly disturbing, given it's a man who starts being terrified by a puppet he himself voices. Plus, some of Scarface's 'deaths' were just creepy, even if it WAS a puppet. Giant fan as a wood-chipper anyone?
It's worse if you were among the minority that weren't fully aware that he was a puppet.
The worst part is that its ambigious as to the extent Wesker is aware of Scarface's true nature. Some versions has him be a slave to a dominant alternate personality that expresses itself through the puppet, others has Wesker essentially faking the whole thing, with his mild-mannered regular persona being an act, and others imply that the Scarface entity might actually be its own being, a supernatural manifestation born from the wood the doll is made of, which was once the hangman's tree of the asylum... And no one knows which one is true, save maybe Scarface himself.
There's also something deeply unsettling about watching the normally cool and collected Dick fly off the rails in "Robin's Reckoning" as he attempts to kill Tony Zucco.
The episode, "The Forgotten", where Bruce is captured by a slave camp, and the attack has left him with amnesia. The episode itself is pretty tame on the nightmare department, except for a particular dream sequence. The still disguised Bruce Wayne stumbles into a room full of mirrors, when all of a sudden he hears his own voice laughing. This leads him to stand before a mirror where the pre-amnesia Bruce Wayne is Laughing Mad. With absolutely no warning, the laughing Bruce turns into the Joker, whose arms break through the mirror and pull Bruce in. They emerge from a skyscraper's window, plummeting towards the ground. As Bruce screams, the Joker is still laughing.
Harley: I've never seen you laugh before. I don't think I like it. Cut it out! You're givin' me the creeps!
Baby-Doll's deranged face as she blasts the fun house mirrors down.
As this review notes, "Critters" is actually a seriously creepy episode.
Maxie Zeus. In the original comics version he was mostly a weird but relatively harmless d-list villain left over from the Silver Age. This cartoon, like it did with Mr Freeze and The Riddler, turned him into a very real threat. Tell me if this sounds unsettling; a mentally unbalanced man who imagines himself to be Zeus of Greek myth, with all the wildly unpredictable behavior that entails, and who also has access to a large amount of financial resources AND a personal weapon shaped like a lightning bolt that he can use to fry anyone who displeases him. The worst part is that its implied that the real Maxie's personality is still intact, just supressed by his Zeus persona, which is shown when his secretary briefly manages to break through to him. In the end, he's locked away in Arkham, which his delusional mind imagines to be Olympus.
Maxie: This is where Zeus belongs...
The climax of Perchance to Dream where Bruce is trapped in his mind thanks to an invention of the Mad Hatter's which gives the dreamer/victim what they most desire. In Bruce's case, his parents are alive, he's engaged to Selina Kyle and somebody else is Batman. At the end, he realizes that he's trapped and unable to wake up...until he realizes that his mind can't imagine his life if he were dead. The Mad Hatter confronts him, saying "What if this is real?" Bruce coldly responds "Then I'll see you in your nightmares!" Before hurling himself off the church bell tower. Yes, Batman was prepared to commit suicide.
"Growing Pains" introduces us to Annie, an amnesiac teenage girl, scared by a man who's stalking her... Who's actually a drone of Clayface which somehow gained sentience. Just imagine being lost, stalked, and then learning you're not even a real person. And if this wasn't enough, we see Clayface absorb her back, essentially killing her. This is both nightmarish and a massive Tear Jerker.
Also, how are we introduced to Annie ? By her being harassed by bikers. Who were catcalling her and acting like they just found a fresh prey. Had Tim not intervened, it's pretty clear those guys were about to gangrape a teenage girl.