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Nightmare Fuel: Sonic X
Most evident in Sonic's Scream Test. Eyes aren't supposed to look like that...
How about the part where Amy gets possessed? Sweet dreams◊...
Episode 26 showing Eggman's iconic method of placing animals into his badniks while they are still conscious, frantically screaming and trying to escape. Granted the blow is lessened when you realize the badnik is E-102Gamma.
For some people, Dark Super Sonic.
OH YEAH, DARK SUPER SONIC. Even Eggman was scared of it, to the point of BEGGING Sonic to calm down. For all he knew, Dark Sonic might've gone on to kill the rest of them.
The three-headed plant dragon that Dark Oak, Black Narcissus and Pale Bay Leaf turn into is absolutely terrifying in appearance. Not only that, it also eats Sonic!Oh, crap.
Episode 60 had an eerie tone to it, even going so far as to have one giant creepy eyeball watching over Sonic, Knuckles, and Amy through most of the episode, and the demonic teeth floating in the air near the end. What's even creepier was that the creepy castle they were in for the whole episode was indeed alive. Granted it WAS just a Metarex, but still...
Episode 73. THE WHOLE EPISODE. It's basically Shadow hunting down Cosmo for the most part and if you're familiar with his strength, speed, and capabilities, then you know for sure you can't stop him from causing harm even if you tried. In fact, this is exactly what the Sonic cast was doing only to get "pushed aside" so easily. Of course, at the end of the episode, the crew was able to stop Shadow from doing away with Cosmo... but still the thought of the ultimate life form trespassing your headquarters with the intent of killing you or a best friend is unsettling.