Kardiac, a giant mechanical heart (with tentacles) that abducts small children for unexplained reasons.
The very episode "Haunted" gives a whole new definition to the word "nightmare", considering how Slade is slowly killing Robin only for Robin to discover that it's his own mind destroying him.
Slade: I am the thing that keeps you up at night, the evil that haunts every dark corner of your mind. I will never rest, and neither will you.
Also the part where Robin has been strapped to a bed so he doesn't hurt himself, only for Slade to appear and approach him with an electric scalpel.
Especially the part with the final fight between Robin and Slade. Robin, Badass Normal who pretty much defines The Determinator as a trope, is getting the hurt laid on him so bad that he is begging Slade to stop.
It also depends what age you are when you watch it, but the way the scene is scripted and lit, it reads one hell of a lot like a rape scene. It's incredibly disturbing.
Then we find out he's doing it to himself.
The ending of "Haunted" is the creepiest part of the entire series. We never find out what triggered the mask.
When Raven first enters Robin's mind, the screen flashes through a series of paranoid images of Slade and the inside of Titans Tower. The last one, however, is a split-second shot of a circus tent with two figures falling. The death of his parents.
Interestingly, Slade almost gets creepier in Season 4. While he still talks like the emotionless Manipulative Bastard he was in the first two seasons, his movements when in combat seem much more primal and at times mimic some downright zombie-esque moves due to being undead. It's downright jarring to compare exactly what he has become to what he was before.
"Aftershock" in itself is creepy, but the most horrific part may be when we discovered the extent of the neural suit's control over Terra. Slade can command her to do anything he wants, regardless of her will, and the suit is literally impossible to remove because it's combined with her nervous system. Granted, Terra was able to overcome that due to great inner strength, but imagine a non-superpowered person being stuck in that suit, at the mercy of a master they hate for the rest of their life.
And the seriously creepy line uttered by Slade:
Slade: She wanted control, and that's what I gave her; my control, her body.
In the episode "Nevermore", when Robin goes into the roof of Titans Tower to tell Raven about her door being broken down, she breaks out into hysterical laughter which sounds just like something out of Higurashi no Naku Koro ni, then she just abruptly stops and goes inside. Hell, the whole episode itself is pretty frightening.
How about that Eldritch Abomination that Raven becomes when she gets angry? Big black tentacles, her eyes all red, she gets really tall. And then there's that thing she turned into to scare Gizmo into helping them. We don't actually see it, but apparently there were tentacles, horns, and dragon-like jaws.
Raven sucking Doctor Light into the magic shadows within her cloak; when he's pulled out at the last second, his face is ash white and all he can do is curl up into a fetal position and say, "So dark. Make it stop. Please, make it stop." The fact that in a later episode, all she had to do was snarl at him and he immediately went into Terrified Surrender Mode doesn't ease the imagination of what might have happened under that cloak. Also note that his armor appears to be crumbling away when he's pulled out. Makes you wonder what the shadows do.
Crumbled? Try chewed...
Starfire going through alien puberty in "Transformation" and the scene in the same episode where she meets the lady who looks like the benevolent DC character White Witch - but who turns out to be a bug-like creature who eats young Tamaranians going through said Chrysalis type alien puberty. Just imagine it. You're being enclosed a chrysalis for reasons you don't understand and nobody can explain, nobody is there to help you, and just as the cocoon closes, you're going to be eaten by an alien.
Beast Boy turning into a monster that resembled the Beast in the episode "Beast Within" due to a mutation-inducing chemical. And it's implied that the chemical unleashed the combined primal instincts of all of BB's most dangerous animals.
Since both Slade and Raven tend to inspire this, there's that scene in "Birthmark" where Slade is sent by Raven's demonic father for no other reason than to torture her about her destiny to cause The End of the World as We Know It? Which he does by shredding her clothes and then tossing her unconscious body off a roof? "Oh... and happy birthday."
Then there's the reveal at the end of the season, after Trigon escaped and razed the entire planet in under a minute: Slade may have returned, but it was only what he had of a soul, inhabiting his undead fleshless, muscleless skeleton, wrapped up nicely in his normal outfit.
Mother Mae-Eye. It's actually a pretty creepy episode, what with zombie cookiemen, the menacing, hopeless music, what could actually be in the pies (They're red, think about it), and there's the Mean Green Mother herself, who is difficult to explain, but scary none the less, think Wicked Witch ofthe West, then give her Mind Control.
Madame Rouge in "Calling All Titans". Robin freezes her, then shatters her into little frozen pieces. She then reforms herself in a manner similar to the T-1000.
In a combination of Paranoia Fuel, Slade laser-injects nanobots into the Titans in season one. Think about it. Thousands of nigh invisible robots floating around in your body, possibly for decades. And what Slade wanted to use them for is a whole other can of scary.
Terra and Raven's mudfight. Sure, it sounds kinky in text, but poor Raven... The episode really drives home the feeling of betrayal through the dialogue, where Terra's cold taunts push Raven far enough that she goes into demon mode, and even that doesn't help her in the fight. She's then helplessly drowned in mud by her former friend, onscreen, the first time one of the Titans in the show actually looked like they were about to be successfully killed off. None of the other fights in that episode are as prolonged or vicious.
The episode "How Long Is Forever?", is the episode where Starfire is sent into a Bad Future and sees everyone's lives in the present destroyed with the dispersal of the Titans following Starfire's absence. It definitely counts as some type of horror. Between seeing Beast Boy as a washed up, depressed, carnival animal, Cyborg as a person that can't even get outside a decaying tower, and Raven going insane to say the episode is unsettling is a major understatement.
Cyborg's circuits and backup power cells had all died out, so he's forced to remain within Titans Tower with the rest of the Titans gone, letting it fall to disrepair as he simply tries to keep himself alive while hooked up to a non-portable power cell that can't even allow him to leave the tower.
Beast Boy attempted the solo hero thing, but turned out too chicken and was beaten up routinely. He decided to resign himself to being "the one-man zoo" at a freak show, so he could cage himself in and protect himself from others as he grew old, a far cry from his start as the Plucky Comic Relief and The Big Guy.
While it was epic, the ending to Mumbo's Villain Song might be considered rather unsettling...
Mumbo: Tonight, I will make the Titans (Dramatic Pause) disappear...(whispering) forever.
Whatever the heck that thing the rest of the Titans were chasing in "Things Change" was.
The episode "Fear Itself". The scariness kicks in when you remember that Raven was the one who made these things without even thinking about it. Yes, the snarky, demonic, demigoddess who's in near constant control of her emotions. Makes you wonder about the extent of her powers.
One particularly unsettling part was the part where Cyborg goes next. Immediately after Starfire's taken by those creatures, Cyborg pulls Raven outside and convinces her to keep moving. After a while, she agrees, and starts walking, while Cyborg just stands there, illuminating the hallway with his shoulder-mounted flashlight. We get a rather creepy shot of Cyborg looking very disturbed, but still looking at Raven's way. We pan over to Raven, and the light turns off. She turns around, and he's gone.
Starfire's "disappearance" scene is pretty creepy- a bunch of what look like mutated rats jump on her, and even though she frantically tries to zap them with Starbolts, there are just too many of them and they drag her down into the ground, and Starfire lets out a terrified scream before getting totally submerged by monsters. And when Cyborg jumps in to try and save her, the monsters part to reveal nothing but the floor beneath them left.
The monster from that episode is pretty creepy too. A green wraith-looking thing covered in black fanged mouths and tentacles.
"The Sum Of His Parts" is quite terrifying. Here's Cyborg, a guy who's had most of his body replaced with robotic parts, and a man named Fixit has kidnapped him with the intent to finish the job. It's a total horror movie premise made even more frightening by the fact that it's not part of the seasonal arc and starts out as one of the more light-hearted filler episodes. On top of everything, Cyborg's worst fear is losing his humanity and when he begs for release on those grounds, Fixit calls his humanity "flawed". Plus, there's something chilling about that mask Fixit tries to replace Cyborg's face with (And at the climactic moment, he presses it on, muffling Cyborg's speech so that no one can hear his screams).
It should be noted though that Fixit did come to realize the error of his ways by the end of the episode and is shown to be helping the Titans in the tie-in Teen Titans Go! comics once or twice.
Even more unsettling is when Cyborg manages to pull aside Fixit's cloak... we see a truly bizarre show of biology: nothing but pulsating/beating organs ala General Grievous... no blood/bones or anything remotely like nerves or muscles, and a deformed third arm randomly jutting out. How Fixit ended up like this, no one knows.
The horrible moment when Slade's mask was knocked off in Season 4 to reveal a monstrous dead skull can freak out even the most tough-as-nails viewers.
In "Hide & Seek," Raven's flat and stoic recounting of most of the season 4 events, which include the aforementioned undead Slade unmasked, global apocalypse, and unfathomable evil that is Trigon to a group of innocent little kids and a toddler. Naturally, all three kids are very freaked out.
Monsieur Mallah actually manages to catch the kids when Raven has her back turned for five minutes. Fridge Horror kicks in when you wonder what would have happened to them if Raven didn't get suspicious and turn back.
Heck, plenty of the villains from the so-called "joke" episodes are actually really creepy.
Mother Mae-eye, a witch with pies that brainwash you, zombie cookies, and the strange tendency to bake her "beloved children" into pies.
Mad Mod, whose hypnotizing machines could turn you into a vegetable simply because you aren't referring to cookies as "biscuits".
Mumbo, who could erase you in a blink by sending you into his magic hat... the list goes on and on.
The Titans' evil doppelgangers, created by Trigon and infused with some of his own dark power to give them an edge in battle.