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.
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 musical cue that accompanies Captain Cutler's appearances in "A Clue for Scooby Doo".
One from the classic show; episode 15 of the first season of Scooby-Doo, Where Are You! features the Spooky Space Kook. The opening of that episode... We have an alien, dilapidated ship drifting eerily across the screen, and then the titular Space Kook, a lumbering spacesuit with a glowing, flickering skull inside its translucent dome, approaches, staring right into the viewer's eyes as it gives out this horrible shrieking cackle.