This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / The Real Ghostbusters
The Grundle, possibly the most terrifying foe from the entire franchise, who is a cross between a vampire, a goblin, and a child molester that kidnaps children in the middle of the night and turns them into more Grundles.
Similarly, the Boogieman. Holy crap.
The really scary part? The Boogieman WASN'T a ghost. He was a demon, which meant the Ghostbusters couldn't stop him with their equipment. And Egon was very terrified of him. Which makes his eventual triumph a Moment of Awesome.
If the appearance of the Boogieman isn't scary enough, his voice when he wheezes "I remember you" to Egon will send chills down anyone's spine, especially when they realize he terrorized Egon as a small child- imagine being a kid and seeing that thing skulk out of your closet and speak to you in that unholy voice on a nightly basis. Eeek.
Ghash, the poltergeist in "Slimer Come Home" that would befriend the ghosts, gather them up, and eat them... and the mouth was at its stomach...
The freakiest part is after Ghash absorbs Slimer and a bunch of other ghosts and you see bulges all over Ghash's stomach as they try to get back out. The Ghostbusters save Slimer, the rest of the ghosts... weren't so lucky.
The Sandman wasn't particularly scary in-and-of himself, nor was his plan to put the world to sleep horrifying...but his horrible, horrible voice sure is.
Theres also Fridge Horror. The Sandman genuinely wants to protect humanity from itself, but what would happen if a natural disaster occurred while everyone was asleep? Answer: countless innocents could be injured or killed and no one would be in a position to come to their aid. And if he put all the Ghostbusters to sleep, no one would be left to stop later paranormal attacks.
Never mind a natural disaster. The Sandman wants the world to sleep for 500 years, everyone would be dead within a month or less as their bodies shut down due to dehydration and starvation
The episode where the ghost-obliterating robot accidentally creates some extremely powerful ghosts from the dispersed PKE. The results were... bad.
A parody of Citizen Kane wound up being extremely creepy, with comparatively low-key hauntings plaguing the Ghostbusters all throughout.
The ghosts in general are monstrous and particularly inhuman.
Cthulhu is extremely horrifying. This show is one of the few to be able to make a Cthulhu live up to the hype of how terrifying he's supposed to be. What's scarier is that he's nearly unstoppable, even with their modern weapons.
The Ghostbusters' sinking realization after they banish Cthulhu that they still have to deal with his cult of murderous psychopaths — and how the timely arrival of the police (i.e., sheer luck) saved their lives from a very mundane threat.
The Old One from "Russian About" was another Lovecraft pastiche. The only thing Venkman could do when he saw it was scram.
The Eiffel Tower sequence in "The Ghostbusters In Paris" had an army of disturbing ghosts, camera angles designed to keep the viewer from seeing them, John Carpenter-esque music, and all the characters saying a version of "Run. Run!"
THAT. MELTING. FACE.
The ghost that feeds on electricity in "Ain't NASA-sarily so".
Egon's horrifying scream of pain when he gets hit by the de-stabiliser beam in "Egon's Ghost".
Mee-Krah from "Standing Room Only". An almost completely unstoppable Eldritch Abomination who mercilessly devours smaller ghosts (who choose imprisonment in the containment unit rather than fall victim to him), leaves deserts in his wake, and nearly smashes and melts New York to ruins, all the while emitting a monstrous growling noise. Needless to say, this was one episode that subverted the Lighter and Softer theme of the later seasons.
There's something very unsettling about seeing ghosts spooky-looking in their own right quivering with sheer terror at the thought of Mee-Krah. Worse, the Ghostbusters throw everything they've got at it and can't even slow it down until the end.
As the title says, "The Thing in Mrs. Faversham's Attic". A force that can possess mere objects, effectively bend reality to its will and full of rage over being confined in that attic for seventy years.
This episode's also notable for having almost no comedic elements whatsoever: there's a bit of Cringe Comedy with Slimer trying to trick the entity by impersonating Mrs. Faversham's late father, but otherwise it's about as straight a horror story as an H.P. Lovecraft tale.
There's also "Mrs. Rogers' Neighborhood", the episode where they visit an old lady who turns out to be a demon that possesses Peter so he'll open the containment unit.
Wat the demon is really nightmare fuel! check it out at 10:04 in this video 
The one where Slimer is befriended by a thing that appears in the form of a Creepy Child.
The Body Horror-riffic episode where our heroes become "allergic to ghosts". Giant body parts on the torso, anyone?
Egon is bitten by a chicken-like ghost and turns into a werechicken.
In another episode everyone in the city got turned into insectoid mutants including Janine who became an insect queen; hers is especially scary because of the weird, womb-like mutation egg Janine was trapped in, from which she broke free from, gasping for air, and screamed in terror because the front of her torso from (apparently) neck to groin had turned into chitin. Also, she begins to look like a praying mantis at one point, which she's coping with, but she apparently still has eyelids.
In "Ragnarok and Roll", the Anti-Villain tries to bring on the end of the world because his girlfriend dumped him. That face in the sky and the guy's nose-less face - gave me nightmares for sure!
How bad was it? The Ghostbusters were willing to sacrifice themselves by overloading their proton packs (which would take out everything in a quarter-mile radius) in the hope that they would be able to stop him.
The demon-possessed Ray, Janine, and Slimer's faces in "Ghostworld". Yikes.