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 2, "Legend of the Gobblewonker". Mc Gucket has made these robots before, and has used them on populated areas just to get attention. As is hinted later, this is probably him being nice.
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 8, "Irrational Treasure". Not only do Blubbs and Durland suddenly become frighteningly competent (And yet somehow remain just as dense), the episode gives us the fear that the people we trust to protect us can turn on us the moment we least expect them to.
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) SMASH!
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.
Dipper's Guide to the Unexplained
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 little 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.
Octavia the 8-legged cow from "Mabel's Scrapbook". She looks harmless enough...until she zaps a passing eagle with her Laser Eyes and eats it with her Overly-Long Tongue.
In one of the trailers of season two, Lazy Susan is seen on a payphone with two men in face-concealing hoods approaching her menacingly, all while creepy music plays.
What's even worse is that it displays a lot more of a malicious personality than a lot of other supernatural creatures. Unlike the numerous monsters that fall under True Neutral, to the Summerween Trickster and Pa and Ma who have a Freudian Excuse, to even Bill who's motives and end goal are highly questionable, the Shape Shifter is a horrifying monster who taunts Dipper about what may happen to him if he goes too deep, transforming into a horrified Dipper before he is frozen in a chamber. Soos even lampshades it with a "good luck sleeping at night."
The build up to the Shape Shifter reveal was surprisingly creepy, even for this show! Dipper and Wendy, separated from Soos and Mabel, run into the "author of the journals". Everything's going fine, Dipper is happy they managed to find him and everything seems to be going okay. Then Wendy realizes that the man they're talking to is the Mascot on the can of beans down in the bunker. Realizing how bad this is, Dipper tries to head out. And then the Shape Shifter takes quite a notes fromanother certain shape shifting alien....
One of the worst parts about the Shapeshifter? He makes the exact same sound effect as the Zurg-a-Tronic Megaray, the source of many kids from the 90s nightmares.
The overall similarities to The Thing also add a lot of Fridge Horror. Wendy's bleeding after the initial fight with the monster...
Whatever that monster in the shadows was. It appears to be a spider, but we never actually see it in full form. It's also mentioned to have regenerative properties... This is assuming, of course that the monster wasn't Experiment 210 and the "author's" battle with it wasn't some sort of ruse to gain Dipper and Wendy's trust, such as shapeshifting part of itself into the "author" and ripping out the monster's tongue.
The Shapeshifter's last words.
You think you're so clever, don't you Dipper? But you have no idea what you're up against. You will never find the author, and if you keep digging, you'll meet a fate worse then you can imagine. And this will be the last form you'll ever take! (As the shapeshifter is frozen it takes the form of a screaming and terrified Dipper.)
"The Golf Wars" was essentially a really funny, light hearted episode, but it did have two moments; when the Lilliputtians tie up Pacifica because they think Mabel would like them best if she had the chance to murder her instead (prompting another group to threaten to murder her golf tutor in retaliation), and when they all decide to work together so they can cut Mabel open. Kind of a surprise.
"Sock Opera". Bill is back. And he's somehow even creepier.
Bipper is, granted, pretty hilarious ("BOY THESE ARMS SURE ARE DURABLE!") but he still manages to be legitimately terrifying at the same time. Bill enjoys causing Dipper's body pain way too much and his expressions when threatening Mabel are cruel in ways Dipper's face should never get.
And somehow he gets even worse in the short where we are introduced to him dressed as a reverend. The incredible contrast, coupled with the dark clothes, his unnatural eyes and (now truly a) Slasher Smile makes him look extremely sinister.
Also, the reveal that Bill can straight up possess people if he can con them into a deal with him (which is exceptionally easy for him to do), even if they have a still living spirit in them. Dreamscaperers showed that he is able to enter minds and mess around, but this is a whole other level of evil and power. If Dipper hadn't been able to possess the sock puppet and warn Mabel about what Bill had done, he could have potentially been left in the Planescape for the rest of eternity.
Worse yet, while most of the time when people make deals with demons, the demons have to keep their end of the bargain, even in a roundabout way, if they want what the human promises them. Bill completely destroys the laptop and still gets away with taking Dipper's body.
Worse still is that Bill did keep his end of the bargain. If you notice, Bill explicitly worded their entire conversation as if they were negotiating a deal. But they weren't, Dipper just assumed so. The deal was "I want any puppet." "Just one puppet?...Fine!" And then he removed Dipper's soul so his body could become Bill's puppet. He just casually outsmarted one of the most intelligent and paranoid characters ever seen on this show, and he made it look easy. Bill is extremely intelligent, crazy, sadistic, and he seems to be working towards whatever he's doing casually. Just what the hell kind of lengths would Bill go to if he ever became serious about doing something?
Perhaps one of the more unnerving things about Bipper is that, until Dipper finds a way to tell Mabel what's going on, nobody who knows Dipper finds ANYTHING strange about the way he looks, talks, or behaves. It's almost as if Bill's Reality Warper abilities convinced them all that was normal.
The possession scene itself gets up here too. It's quickly Played for Laughs as Bill gets used to a physical body, but the music that starts playing combined with Dipper's screaming combined with Bipper slowly climbing to his feet as all the lighting goes red is pretty terrifying.
The animators seem dead-set on upping the amount of body-horror the show has. Bill conjures an eternally screaming head for no reason other than to frighten Dipper. Then he snaps his fingers and the head unravels, stripping away hair and skin, then flesh and eyes, and finally pulling the skull out of frame. The head is of course screaming the entire time.◊
Looking closely, the head's tongue ties itself in a knot as it unravels.
Bill's appearance when Dipper wishes for some clue or hint for the password. The full moon rolls over and is revealed to be Bill's eye.
In the Season 2 trailer, we see a group of animatronics that attack the main group during "Soos and the Real Girl." However, one of the animatronics looks eerily similar to Mabel's puppet, Bear-o...
In that episode, we're treated to an old coin-operated machine in the Mystery Shack that malfunctions and spews oil from its face while screaming, which terrifies a poor unfortunate little boy to tears.
The episode itself centers around Soos coming across a Yandere dating sim that ends up possessing the aforementioned animatronics to get to Soos and "delete" Dipper, Mabel and Melody.
Speaking of that Yandere dating sim, how about the split-second Nightmare Face Giffany pulled after Soos paused her and pulled out her disc to take it back to the game store? If there was any doubt about whether she was being a temperamental Tsundere stereotype (as one may expect of a Japanese dating sim), or going full blown psychotic Yandere on him, that look probably sealed the deal. Here it is for all its horrifying glory◊. It even resembles a face Gasai Yuno from Mirai Nikki pulls.
It's also implied that Giffany killed her creators.
Implied nothing, they show that she electrocuted anyone who tried to destroy her.
Her death is nothing to sneeze at. Basically, she utters a really horrifying scream and the robot she was possessing melts. Geez.
Any one that has been in an abusive relationship will tell you that Giffanys speech to Soos about real women will only judge and insult him and that staying with her is the only way to prevent being alone hits a little too close to home to what their abusers have said to them to get them to stay.
Game companies needed to produce many, many copies of a game to recoup the expenses in creating a game in the days before direct download. How many other players are dead, trapped in the game, or forever under Giffany's digital thumb? And what happened to the three people who owned the game before Soos?
This episode is frightening because unlike Rumble McSkirmish, Giffany thinks. She's not locked into a set of rules like Rumble is. She's a living, thinking entity capable of complex planning and emotional manipulation. Move past her screaming match when Soos says he's leaving her to the end of the episode; she goes right back to being her charming self, gleefully describing to Soos how no real woman would ever be with him, but how she's always predictable no matter what. You can tell by the look on Soos' face that Giffany knew exactly where to hit, and that, even for a brief second, Soos really considered giving his mind to Giffany.
Watch the dumpsters when Stan is being attacked by the badger robot. One has Robbie's "explosion" painted on it, but the second has a much more sinister symbol◊.
Not related to Giffany, but the animatronics at the Suck E. Cheese's knockoff restaurant were pretty creepy to look at even before they were taken over. It doesn't help that one of them looks disturbingly like Mabel's puppet Bear-O.
On a similar note, some of the things that they have built into them don't really make a whole lot of sense, like the clawed hands on the Barrel Rat Robots. Considering that they looked like they were all endoskeleton they obviously weren't meant to be seen, making one wonder why they were even put on to begin with.
I doubt the female animatronic that Giffany possessed actually had a device that could upload people's brains. It's probably supposed to show the kind of power Giffany has at her disposal.
Although it's a complete coincidence (as the episode was finished long before the game came out), the animatronics have reminded many people of the indie horror game Five Nights at Freddy's.
The woman Soos accidentally knocked over in the mall was pretty creepy as well.
You can't undo who you are.
Episode 6: Little Gift Shop of Horrors has an unnamed person being greeted into the Mystery Shack late at night. After Stan tells three different stories about some of the items he's selling, the person decides not to buy anything. Then Stan gives them a "potion" that knocks them out and we get to see them wake up in the shack the day after, trapped inside a case and apparently glued to the stand, being shown off as an exhibit called "The Cheapskate". Kids show, right?
The above is made worse by Stan's continued creepy smile as the person's vision blurs and they fall over
"You shoulda bought something while you had the chance..."
Arguably even creepier is what happens afterward: Mabel and Dipper see the person in there, and do not seem to care at all. Sometimes there's a thin line between Rule of Funny and Rule of Scary.
Though if the cryptogram at the end is to be trusted, this episode is non canon.
One of the items Stan talks about is this some... blob creature... with an unnatural appearance and high amount of eyes and other orifices.
The swarm of disembodied hands.
You thought the stop-motion monsters were creepy? Well, say hello to TO MABEL'S CREATION! THAT THING SHOULD NOT EXIST!!!
For those who don't know, Mabel conquers her fear of claymation and eventually changes the clay cyclops into something she likes. The end result is she ends up making the the Shimmery Twinkleheart, who is somehow even more terrifying rendered in claymation than in regular animation.