Might just be a funny coincidence, but in the Bob's Burgers episode "The Belchies", Louise (voiced by Kristen Schaal) sarcastically lists a grappling hook among ways to get herself out of a pit trap. In Gravity Falls, what's the free item Mabel (also voiced by Schaal) chooses from the Shack's Gift Shop? A grappling hook gun.
"Sascrotch" might just be a Cinema Snob reference, as he mentioned in his review of "The Geek" that it would be an "amazing title" for a Sasquatch porno.
The title is a play on the 1917 silent film title "The Hand That Rocks The Cradle".
According to Gideon's voice actor, Thurop van Orman, he's a parody of tent-revival "miracle healer" televangelists like Benny Hinn. The name "Gideon" is therefore most likely a reference to the Bibles published by Gideon International and distributed in hotel and motel rooms.
Gideon also means "Feller of Trees" in Hebrew. Trees, Pines. Dipper and Mabel Pines. Get It?
The room◊ where Dipper meets Lil' Gideon is straight from◊ Twin Peaks. Gideon (white hair, blue suit, white shirt) is even a Palette Swap of The Man From Another Place (black hair, red suit, black shirt). The Club also appears to be influenced—at least in name—by "One-Eyed Jacks".
Episode 5 features a possible nod to Phineas and Ferb, with Dipper using one of their catchphrases. Wendy tells Dipper that he's really mature for his age. Dipper's response:
The puma and panther shirts that the customer compares resemble those of The Mountain T-shirt brand.
Dipper's favorite song is "Disco Girl" by Icelandic Pop Group BABBA, the tune of which is nigh-identical to "Dancing Queen".
The bag of Jerky that Dipper gives to the Manotaur is nod to Slim Jim complete with a "Macho Man" Randy Savage/Hulk Hogan like Wrestler on it.
Upon reading the jerky's slogan ("You're inadequate!"), Dipper replies, "You said it, brother." Hulk Hogan is famous for using 'brother' a lot.
Dipper clones himself several times, and one comes out wrong because of a paper jam. The malfunctioning clone then claws at people's faces while making sounds reminiscent of Doodlebob, the warped, homicidal copy of Spongebob from an episode of SpongeBob SquarePants.
Also very similar to the episode of Phineas and Ferb in which Doofenshmirtz creates multiple copies himself. Guess if he had a failed copy. Funnily enough, one of Doof's failed copies was due to a paper jam.
Steve, the local mechanic, won't help Stan with his car, because he insist on pretending that he's a 1863 pioneer who has no idea what a car is. This is very similar to the South Park episode "Super Phun Thyme", where historical-reenactors at the local Pioneer Village refuse to break character no matter the circumstances.
When the twins travel into the past, Dipper asks "When are we?" Mabel is about to ask the same question. This is a reference to Back to the Future when Marty asks "Where the hell are they?" and Doc Brown replies with, "The question is, when the hell are they?" Dipper said the line Mabel was about to say, as she expected him to start with, "Where are we?", thereby copying the exchange word for word.
There's an arcade in Gravity Falls, so there are lots of video game references and shout outs to be made. The three games seen in the arcade, aside from "Fight Fighters" listed below, are parodies of Frogger, Pac-Man, and Dance Dance Revolution.
Soos plays Nort: The Game Based On The Movie Based On The Game. He even plays a game similar to the light cycles, only with Segways. In addition, when Soos, enters the game (i.e. he opened the back, and got stuck inside), a customer happens upon his face pressed against the screen ranting about how "It's not just a game anymore!"
Nort's controller also looks similar to the controller from Gorf.
Rumble breaks into a barrel factory and starts throwing barrels at Robbie, who has to dodge them a la Mario in Donkey Kong.
Rumble about to "finish" Robbie and the music that plays during Dipper and Rumble's fight are both nods to Mortal Kombat.
One sequence features Rumble destroying scenery like streetlights and fire hydrants before a flashing "GO" arrow appears, allowing him to proceed to the right. These are shout-outs to the Beat-Em Ups produced for arcades and home consoles in the late 80's and early 90's, like Final Fight, Streets of Rage, and Double Dragon.
The credits are a shout out to Super Mario Bros. 2 Character Select screen complete with Mabel quoting Mario. Grunkle Stan completes this by immediately saying "I'm slower, but I jump higher!", in reference to Luigi. Then they are eaten by Soos's head as Pac-Man.
With a healthy dose of the Batman villain Scarecrow (In the hat and jacket) for good measure.
Stan trying to scare trick-or-treaters by having Waddles pretend to burst out of his chest is an Alien reference.
It's done twice in this episode, actually. At the very end, Soos does it to the Summerween Trickster, and it's no less obvious. It's also done in nearly the exact same way as it did to Stan.
In one scene, the young boys tell Stan that they're not afraid of him. He responds by saying, "You will be. YOU WILL BE." This is a reference to Luke Skywalker and Yoda in The Empire Strikes Back.
The scene where they hide from the Trickster in the Summerween store is highly reminiscent of the kitchen scene in Jurassic Park.
Stan discusses with a few young boys what can scare them, and they show him a video of a cute little kitten, which is abruptly cut by a screaming woman. This is a reference to the rather popular Screamer Prank videos, where a seemingly normal videos is abruptly cut by a creepy image.
The kid who shows said screamer somewhat resembles Nelson Muntz
The lifeguard shouts to Dipper: "If one more supply gets taken, YOU'RE FIRED!" The way he says it is absurdly similar to Benson, and considering that the creators of both shows are friends in real life, it was probably intentional.
During the slumber party, Grenda starts whacking the ground out of happiness, just like the title character in Wreck-It Ralph.
The novel "Wolfman Bare Chest" is most likely a parody of Twilight.
The title is a play on "Carpe Diem," Latin for "Enjoy the day" or "Seize the day."
Soos makes an allusion to Tetris when explaining how he fits in his break room.
At one point, one of the boy-clones is commanded to dance, and starts doing moves from *NSYNC's "Bye Bye Bye" music video. (Especially hilarious since Lance Bass himself is one of the voices.)