Didn't think it was possible for a Disney series to venture into this territory? Ha ha, "Welcome to Gravity Falls" indeed.
The creepy whispering in the intro, along with those unsettling chords and flickering subliminal imagery, and the dying/fading on the last note, from the intro will never cease to send a chill down your spine.
It's "Three Letters Back" in reverse — the cipher for the initial end-of-episode codes. It eventually switches to other messages when the cipher changes accordingly.
STAN IS NOT WHAT HE SEEMS
Episode 1, "Tourist Trapped". A bunch of gnomes wanted to kidnap and marry Mabel, a little girl, which is unsettling as it is. That's not even considering the fact they can be old even by human standards.
They were rather feral when Dipper comes to rescue Mabel, one of them attempting to eat Dipper's face off.
And then there's the big gnome monster that they all form together...
Episode 3, "Headhunters". Wax Sherlock Holmes tried to outright murder Stan with an axe.
Episode 4, "The Hand That Rocks The Mabel", when Lil Gideon shows his true colours. He's unstable, violent and seems to believe that Mabel is secretly in love with him. Heck, he tried to cut out Dipper's tongue and kill him just to get to Mabel. And keep in mind Gideon is three years younger than Dipper!
It doesn't help for the fact that Gideon has the voice of Flapjack and while he sounds a tad goofy, it also proves to be quite unsettling.
Episode 5, "The Inconveniencing", has so many...
POSSESSED MABEL. It's creepy enough in concept, but actually seeing it...
Alex Hirsch's response when asked about the monster if it'll ever be explained? "No."
When Dipper turns around and sees that his and the others' reflections have become skeletons.
The fates of the teenagers that the twins venture to the store with: Being trapped inside a television screen, a video game, a cereal box cover, and a hot dog that's being cooked.
And judging by the sound effect and reactions of the characters watching, the cereal box one was a Gory Discretion Shot.
Cereal Box Bird: I'm bonkers for eating you alive!
More "Getting Crap Past the Radar" than nightmare fuel. But it's really really surprising the show was allowed (being Disney) to get away with using the word "Murder" and showing two corpse outlines. Darker and Edgier Disney indeed.
Episode 6, "Dipper vs. Manliness" we're introduced to the leader of the manotaurs! Only for him to be DEVOURED on screen by the real leader SECONDS later. While on its own the scene isn't so bad, but you must think of how Dipper must feel knowing these creatures REGULARLY eat their own as offerings It's implied that this isn't the first time this has happened. Doubles as a Moment Of Awesome when he finally stands up to them however.
When the Leader pulls a spear out of his chest with screaming and blood and everything. Uhhh...
Episode 7, "Double Dipper", has two that particularity spring to mind. Firstly, the the copy of Dipper's (dismembered) arm bubbling and melting away, and secondly, Paper-Jam Dipper.
How about Dipper's dismembered copy arm in the first place? Think about it? A disembodied arm crawling towards you, not to mention the music that was playing in the background of that scene.
Paper-Jam Dipper welcomed his death. Apparently he was suffering from his deformities.
Episode 9, "The Time Traveler's Pig", has the Time Baby, a large headed, red eyed baby that seemingly controls all of time.
The way Gideon screams at his parents, demands his father look him in the eye and grabs him by the face, etc., are all strongly reminiscent of a habitually abusive parent lashing out at a child rather than simply an outrageously bratty kid acting out.
Gideon: Heh heh heh...Hahahahah! WHAT AM I DOIN'!? I don't need ransom! I have this! I'll just shrink Stan and take the Shack by force! And if the rest of you get in my way... (Rips heads off Pines family figurines) Wham!
Episode 12, "Summer-Ween", has a monster who tasks Dipper and Mabel with bringing him candy, or he'll eat them. He's scary enough at the start, but his transformed state is even scarier.
And to demonstrate he's not kidding, the Summerween Trickster grabbed a random kid and ATE HIM WHOLE! And this is the first five minutes of the episode!
The Summerween Trickster's actual face behind the mask.
How much the Trickster looks like Noh-Face without his costume.
Stan's attempts to scare the two Trick-or-Treaters are kind of scary, even if the kids don't think so. His first attempt is to wear a mask that makes it look like his face is melting off his skull.
Episode 13, "Boss Mabel." That poor, poor couple Dipper caused to go insane by looking into the Gremloblin's eyes. They're last seen carried away on stretchers in catatonic states, with their eyes wide in frozen terror. Yes, Disney openly admitted to Mind Rape on this show.
The dead, mummified looking merman◊ seen in episode 1 becomes extremely unsettling now that the twins have learned merfolk are real, intelligent beings.
Most likely it's intended to be a reference to the Fiji Mermaids, a common carnival attraction about a century ago. Mind you, they were nightmare fuel in their own right, and usually consisted of a mummified ape sown together with a fish. Of course, the one shown in this episode IS human sized...
The kid in the pool filter when you think about it for too long.
Episode 16, "Carpet Diem." Soos is switched with Waddles, and while he's being hunted by Old Man Mc Gucket, Waddles is off screen. Whatever he was doing, it resulted in a marriage proposal with a woman being so unbalanced that a mute, bumbling man with no indication of sapience can go from total stranger to marriage material in the space of a few hours — and when he does start behaving like a human being, she's no longer interested.
Some of the creepy expressions Waddles makes while in Soos' body.
Episode 17, "Boyz Crazy." The sole fact that the producer of Sev'ral Timez has genetically engineered the band and KEEPS THEM LOCKED IN AN OVERSIZED HAMSTER CAGE is kind of frightening.
The clones kept in test tubes. There was an adult, an older kid, a younger kid, a baby... and a fetus.
Robbie brainwashing Wendy with his song. The backmasked message itself it pretty damn creepy, too:
Low Voice: You are now under my control. Your mind is mine.
Plenty of scare chords related to that above message.
The manager of Sev'ral Timez. What a bastard. It's clear he's abusive to the people he creates.
The shit-eating grin Robbie has on his face before he brainwashes Wendy with his song. He knows damn well that what he's doing is despicable and disgusting.
Sev'ral Timez is released as babes in the woods. Candy says casually, "They won't last a week."
Episode 18, "The Land Before Swine". When the Mystery Shack gang first comes across the pterodactyl's nest, several skeletons are seen nearby.
As the gang runs from the pterosaur, they pass a T. rex stuck in amber that wriggles its arms, suggesting that it might free itself someday.
Also, Old Man McGucket getting swallowed alive by the baby pterodactyl, and implied to have eaten his way out of it at the end.
There's also the general fear of having a beloved pet being snatched away by a predator.
From Episode 19, "Dreamscapers", we have:
The fact that Gideon wants the Shack so badly that he summoned a demon to do it. Not a "spirit" or a "monster" but an actual demon. There's also the fact that the page about the demon in Dipper's book is bloodstained.
The way Gideon summons Bill is with backmasked words. But if you reverse it, he's actually saying "Backwards message". Still doesn't make the actual scene any less creepy, though.
The fact that the unknown author of the journals specifically noted not to EVER summon Bill. Out of all the horrible things that haunt GF, this being scared the author the most. Its entirerly possible Bill is the "Him" the author speaks about in the first episode that is watching him.
Mabel losing her cuteness...it's really not pretty.
Gideon's glowing eyes and freaky incantation while summoning Bill.
Before the episode even aired, Bill was a source of unnerving content. On Disney's website for Gravity Falls, the game "Rumble's Revenge" yields twelve special cryptograms. When transcribed, they read:
"i bet you're wondering who I aM."
"i don't give up answers easilY.."
"i kNow things. Fascinating things..."
"your reality is a game to me. And I like gAmes...."
"mischief is my Middle name, but not my first....."
"thEre are six hints I will give you......"
"1. there is a secret socIety in Gravity Falls......."
"2. the Handyman knowS more than he thinks........"
"3. gideon has Been searching for something........."
"4. what goes up Is sure to come down.........."
"5. dipper is pLaying with fire..........."
"6. i will be returning to Gravity FalLs............"
Episode 20, "Gideon Rises":
The opening sequence.
Gideon screaming at Waddles to get back in the corner, coupled with his terrified expression.
Gideon still retains his Yandere tendencies, and uses the aforementioned Gideon robot to grab Mabel and demand she be his queen.
In "Lefty", Dipper spies upon a man who never turns right and literally does everything left. Then Dipper later gets him to turn around and HE'S NOT HUMAN BUT A ROBOT CONTROLLED BY TINY GREEN CREATURES!!!! The huge reveal was really creepy and completely unexpected.
Watching all of the shorts and then putting the pieces at the end of them together nets this wonderful image◊.
Not to mention when you decrypt the Red Code along the edge, it spells I WAS SO BLIND, HE LIED TO ME, THE DARKNESS IS NEAR.
If you think about it for more than about a second, Gideon's status in prison shown in the first Gravity Falls Public Access short becomes this. He's clearly got a huge amount of influence, and the people he's lording over are clearly pretty unstable, and coordinating a mass breakout is hardly beyond his means...
That aside, the fact that a child who might be no older than 10 would be put in a maximum security prison with people who have probably done some horrifying things to end up there seems like a big concern.