After watching "Vampire Bats and Scaredy Cats" (The Scooby-Doo Show), this troper, as a young child, had to sleep with a full head of garlic on her nightstand. For a month. Literally had nightmares about vampires coming to kill her.
In "To Switch a Witch", the townsfolk decide that a friend of the gang is a witch and were going to torture her to make her confess, Salem-style. Shaggy and Scooby take the brunt of this, which could have gone worse were they not Made of Iron. And the townsfolk never were shown to apologize for this when proven wrong, or even prosecuted for what amounts to assault.
One classic ad on Cartoon Network featured characters from Scooby-Doo: Shaggy showed up in a spooky castle calling out, "Scooby-Doo! Where are you?" This cut to Scooby on a tropical beach, saying, "Right here, Raggy! On Rartoon Network!" What was scary about it was not only the notion that Scooby would desert his friends in the middle of a case, but also the fact that Shaggy was barely animated at all, paralyzed and semi-slouched in seeming defeat as he called for help. It was haunting.
The Ghouls getting Revoltized in Scooby-Doo and the Ghoul School, specifically their expressions: Sibella's eyes shrink as if she were going feral, Elsa looks like her mind just got fried, Phantasm quickly loses her Genki Girl composure and scowls for the first time in the whole movie and Winnie howls for some indiscernible reason. Elsa, Winnie and Tanis were freed early, but Sibella and Phanty remained under the spell longer. The former was freed by Tanis and apparently needed a few seconds to shake off the effect. Phanty, being under the longest, probably would've had more permanent effects had Scooby not knocked over random chemicals in the potion.
Tanis: Gee... you were under the hairdryer so long, you were getting cranky.