Please don't list this on a work's page as a trope. Examples can go on the work's YMMV tab.
Nightmare Fuel: Princess Tutu
Warning: The majority of the more disturbing scenes take place in the second season, so spoilers will abound.
Drosselmeyer's sudden appearances can be quite frightening, especially when he appears as certain objects, like buildings or fountains.
Duck's loss of identity early on in the series, as she grapples over who Tutu is in relation to herself and whether she's just a part in a story or not.
Perhaps the creepiest scene in the entire series is when Rue, after the Raven attacks her, comes "home" to a slightly too-friendly evil Mytho. He wraps his arms around her waist, and talks to her about him sacrificing his heart to the Raven when he completes it. While he cuddles her hand, she takes out a knife and prepares herself to take out his heart so it won't come to that, even if it will kill him. She's about to plunge the knife in when he murmurs, "When you gouge out my heart, give it a kiss, and dye your lips red with my blood! She drops the knife, and their shadows merge into the Raven Prince's silhouette.
Then there's the last two episodes, where the Raven's blood rains upon Gold Crown Town, turning all the peaceful townspeople into ravens that attempt to peck out Mytho's newly-restored heart. Their chant of "Give us your heart!" starts out unsettling and gets worse the more it's repeated.
Not only do Pique, Lilie and Mr. Cat suffer this fate, but a quick scan of the crowd in the finale shows everyone did. Every minor character nearly murdered several of the main cast. They weren't even aware of it.
Who could forget Drosselmeyer, the gleeful master of tragedy who escaped death by writing a story of his continuing to control his world after his death with the bleeding stumps of his arms when the bookmen cut his hands off? His startling appearances adds to the creepiness of his slow disintegration from narrator/weird commentary guy to malicious writer-god.
Then there's Fakir's backstory. Those ravens that seem ever-present whenever battles or foreshadowing's afoot? The ones that congregate on rooftops and are generally unnoticed? Yeah, they rip people to pieces occasionally, and everyone would be concerned if the story didn't hold them in. The townspeople sort of know, but mostly ignore the "outbreak" of ravens that has apparently lasted for nine years.
The scene in the cemetery where Rue finds out just what she's done to Mytho.
The fact that Drosselmeyer's ultimate plan was instating a Vicious Cycle so the main characters would be trapped forever in the town. That means for as long as he wanted, Rue would watch her boyfriend turn into a monster, Ahiru would drown herself in the lake, and Mytho would have to cut out his heart before the whole thing started over. And knowing Drosselmeyer, he'd probably make them aware of all this just to watch them go insane. Thank god Fakir turned out to be a Spanner in the Works, or this would've been a depressing finale.
That or he'd repeat the cycle with different people aside from the Prince.
The fact that if the Story has need of them, people just appear at the gates and disappear when they're no longer needed.
Drosselmeyer's clockwork world, full of clown-like puppets and nothing else. When Princess Tutu is taken there, even the story stops, and he simply makes her dance for him as a puppet and tries to force her into a Sadistic Choice.
Fakir's experience with the Oak Tree. He goes through a mind-screwy sequence and almost turns into a tree.
Earlier, Autor gets electrocuted by the rock Fakir was meditating at.
In Akt 22 Fakir almost gets his hands cut off.
The musicused when Drosselmeyer is angry or up to something sinister. The latter's heard in episode 25 when Fakir tells Autor that Drosselmeyer forced him to write a story about Duck trying to drown herself.
Episode 24 has the Demon Raven's revival, set to Danse Macabre, and Mytho attempting to feed the Raven his heart. Rue and Tutu try to stop him but he shoulders on past, cawing and flying freely to his doom.