The repeating "It's Doc Gerbil's World!" song that sounds like the demented cosmetics themed version of "It's A Small World After All" during the boat road in "Human Habitrail".
The "Freaky Fred" episode. The most disturbing scene is when Fred and Courage are locked in the bathroom together and Fred shaves Courage with a manic grin on his face while a haunting chorus of "la-las" starts to accompany the already eerie music.
"RETUUURN THE SLAAAB!"
"You're not perfect"
Katz's Leitmotif, a smooth but unnerving jazzy beat that always plays whenever he's onscreen and overrides any other background music..
In Twilights Kingdom Part 1, Tirek's magic drain is accompanied by a rather chilling screeching sound. In Part 2, his theft of Discord's chaos magic is accompanied by a distorted, possibly reversed version of his normal drain sound effect.
Played for laughs in a Rocko's Modern Life episode, where the gang is shown walking in a forest and they suddenly heard a noise, freak out, and shout "What was that?!" Filbert calmly walks past them saying, "Oh, just a twig snapping", which turns out to be true.
Roughnecks: Starship Troopers Chronicles does this in one episode, in which Rico hears a mysterious and creepy grinding sound while in a recovery vat after sustaining heavy injuries in battle, a sound no one else can hear. His crew and the medical team working on him all worry about his mental health, until bugs emerge in the base and they realize he could hear them tunneling in.
The gunshot noise Maggie's pacifier makes at the end of "Who Shot Mr. Burns?".
There's a whole room full of scary pacifiers about three-quarters of the way through "A Streetcar Named Marge", when Homer comes to pick Maggie up from the daycare center. Why are they scary? Well, they're literally the only thing on the soundtrack. They're echoing ominously. And all the babies are staring glassy-eyed at Homer.
Sideshow Bob, on occasion. "Hello, Bart..." -> Cue terrified scream....
The loud buzzing sound that came with the live-action deerfly close-ups in the episode "Wormy".
In "SB-129", Squidward travels through time and ends up in a blank white void. He remarks to himself that he can finally be alone... which is when the word manifests itself as a colorful caption. Then a series of disembodied voices start saying the word "alone", accompanied by more colorful representations of the word, until Squidward finally snaps and tries to get out. Just those calm, echoing voices that repeat the word "alone".
The squeaky boots and Mr. Krabs.
The grinding noises that accompany SpongeBob's transformation into SpongeSnail.