When the Shape Shifter first reveals itself to Dipper and Wendy, it takes the form of an upside-down spider-like creature with a long worm-like neck attached to man's snarling head. This is a reference to the 1982 science fiction horror film The Thing, where the titular shape-shifting alien adopts a very similar appearance in a scene.
The entire episode is an allusion to Faust. In the tale of Faust, Faust makes a deal with the Mephistopheles (The Devil) in which he gains all the knowledge of the world, but he will lose his soul in ten years to Mephistopheles. Faust with the help of a maiden, outsmarts Mephistopheles. In the episode Dipper makes a deal with Bill Cipher in which he has to give up a puppet for a hint to the laptop, and in the end Dipper and Mabel both outsmart Bill.
A poster, "HE'S GOT ATTI-CUBE," which has a COOLCUBE logo at the top that is a cube made of C's, a parody of the Nintendo GameCube whose cube is made of G's. The running cube on the poster also resembles a Rubik's Cube and 7-Up's old mascot, Cool Spot.
Stan saying "I'm gonna get that badger," is a reference to the famous, recurring line said by Elmer Fudd about Bugs Bunny: "I'm gonna get that wabbit (rabbit)."
The fact that Giffany killed her creators after becoming sentient is a nod to GLaDOS from the Portal series. Giffany's animation depicting a bunch of stick figures at computers greatly resembles similar animations played in Portal 2.
On Giffany's screen, the binary code translates to "SPACEJAMTWO." This is a reference to the film Space Jam and how it may be getting a sequel sometime soon.
Soos not knowing how to pronounce Giffany's name is a nod to the arguments online on how to pronounce the file type .GIF.
The cryptogram at the end slide is a parody of the theme song of the DiC/CWi dub of the anime Sailor Moon. "WINNING HEARTS BY DAYLIGHT! / POSSESSING ROBOTS BY MOONLIGHT! / HER EMOTIONAL BAGGAGE IS A REAL FRIGHT! / SHE HAS THE ONE NAME GIFFANY." Similarly, the first four lines of the DiC/CWi's Sailor Moon theme song are "Fighting evil by moonlight / Winning love by daylight / Never running from a real fight! (or 'With her Sailor Scouts to help fight' in a later verse) / She is the one named Sailor Moon!"
The idea of Giffany being a stalker and obsessed with Soos is a reference to the "yandere" trait in Japanese animes, giving in the fact that the director, Matt Braly and his girlfriend are being joked as "weeaboos".
The poster of Gabe reads "Master of Puppets: He'll Pull You're Heartstrings!" This is a reference to the song Master of Puppets by Metallica, which contains the lyric "Master of Puppets! I'm pulling your strings!"
The episode's title is a reference to the book Ender's Game.
When Dipper and Mabel enter the Globnar arena, a man can be seen falling infinitly through two portals. This is a reference to an internet meme from the Portal video games in which the player can use a portal gun to place to portals directly above and below each other and jump into them, falling infintely until one portal is moved.
Some signs in the background in the future say "Time Baby is Watching," a reference to George Orwell's book 1984, in which numerous signs say "Big Brother is watching".
Lolph and Dundgren are based on the actor Dolph Lundgren, and their uniforms are similar to the outfit worn by Lundgren's character Andrew Scott (aka GR13) in the film Universal Soldier.
The "Used to be About History Channel" is a parody of the History Channel, which initially focused on broadcasting documentaries and historical fiction series before they began to primarily show more non-historic programs, such as contemporary reality shows and sensationalized pseudo-documentaries.
McGucket's house is virtually identical to Steve Jobs' house.
There is a poster in McGucket's old home, which shows a colorful, bitten-off strawberry similar to the Apple logo, and the words "Ponder alternatively," which is a play on Apple's slogan "Think differently."
The title and the game in this episode is a parody of the popular role-playing game Dungeons & Dragons.
Like D&D, Dungeons, Dungeons, and More Dungeons use an assortment of polyhedron dice.
The 38-sided die is based on the 20-sided icosahedron die used in Dungeons & Dragons to resolve most rolls. There are no 38-sided die used in any real life RPGs; the closest is a 30-sided die, but this an unusually rare and impractical type of die.
A scene where Stan ends up swatting a fairy on his back has it saying "Hey! Look! Listen" which is a reference to Navi, a fairy character from The Legend of Zelda: Ocarina of Time, that is known for using the phrase "Hey! Listen!" constantly.
When Stan presents his taxidermy of Duck-tective, the violin riff originating from the film, Psycho, plays.
Stan describes Duck-tective as: "A TV show that has big mystery elements and jokes that go over kid's head's" which is a meta joke on Gravity Falls.
Additionally, when the Pines family, Soos, and Grenda are disappointed with the Duck-tective season finale's plot twist, Soos mentions predicting it a year ago. It is a reference to how fans of Gravity Falls predicted Stan having a twin brother which was confirmed two episodes previously in "Not What He Seems."
The fantasy names posted up on the boards in the living room by Dipper and Ford are all parodies of names from The Flight of Dragons, an animated movie adaptation of Gordon R. Dickson's book The Dragon and the George. (Jason Ritter's father, John Ritter, was the voice the protagonist, Peter Dickenson, in the movie.)
Gorbasch- there's a human/dragon character named Gorbash in both the book and movie.
Smerghol- Smrgol, another dragon from the movie adaptation.
Omhadawn- the evil wizard Ommadon, from the movie adaptation.
When Bud Gleeful gives his speech at the Town Hall, he gives everyone in the room fifty percent discount on a used car. This is an allusion to Oprah Winfrey's famous car giveaway on the September 13, 2004 episode of the The Oprah Winfrey Show. Bud's line "You get half off a used car, you get half off a used car" is an allusion to Oprah's line "You get a car, you get a car".
Stan's campaign slogan "Yes We Stan" parodies Barack Obama's 2008 tag "Yes We Can."
Stan's "One does not simply" meme is a reference to the popular internet meme of the same name, both of which are based on a quote from the first Lord of The Rings movie, in which Boromir says, "One does not simply walk into Mordor."
Stan walking down Main Street is similar to the "Staying Alive" scene from the film Saturday Night Fever.
The monitor worn by Bud Gleeful is based off of Krang from Teenage Mutant Ninja Turtles.
The poster in Gideon's cell of a picture of a cat hanging onto a branch that reads "HOLD ON TO THAT BRANCH OR DIE, CAT!" is a reference to a well-known poster of a cat hanging from a branch that reads "HANG IN THERE."
One of Soos' lines, while being controlled by Mabel, was "I can promise you a kitten in every pot!". This is similar to Herbert Hoover's presidential campaign slogan in 1928: "a chicken in every pot and a car in every garage".
Mabel asks Ford if he is sending her and Dipper who are finally of age to wizard school, and if there is an owl in his bag. This is a reference to Harry Potter and how the titular character was accepted to magic school once he reached of age and recieved an owl as a present.
When hit with fairy dust, Celestabellebethabelle exclaims, "What the hay!", which is a common "swear" in the TV series, My Little Pony: Friendship is Magic.
Grenda says "Join the Dark Side!," a clear reference to Darth Vader's famous quote in the Star Wars franchise.
During Mabel's montage, one shot shows Mabel, Candy, and Wendy in a shopping cart, with Grenda holding an old woman on her shoulders in the background. This shot is an allusion to the DVD cover of the direct-to-DVD movie Foodfight!
When Ford says "So this is how the world ends. Not with a bang, but with a boop, boop," he is referencing the last line of T.S. Eliot's poem The Hollow Men, "This is the way the world ends. Not with a bang but with a whimper."
Bill saying "The being whose name must never be said." is a reference to the one of the famous epithets referring Lord Voldemort from the Harry Potter franchise.
The center where Dipper tries to punch Bill but is sent flying back mimics a similar scene in the first Pokémon movie where Ash Ketchum tries to do the same thing to Mewtwo but ends up with the same result.
When Bill and Gideon said "Hench-Maniacs, Roll out!" and "Discount Auto-mart Warriors, Roll out!" respectively, these lines refers to the famous catchphrase of Optimus Prime from the film Transformers where he says "Autobots, Roll out!"
During the Weirdness Bubble car chase scene, when Dipper and Wendy are drawn anime style, Spritle and Chim Chim from the TV series Speed Racer are seated in the back seat of the car.
When Dipper, Wendy, Gideon and Ghost-Eyes are transforming in the Weirdness Bubble is similar to Gumball, Darwin, Anais, Nicole and Larry transforming whenever Richard presses a button in The Amazing World of Gumball episode "The Job".
One of the monsters from the Nightmare Realm resembles Cthulhu from H.P. Lovecraft's Cthulhu Mythos, seen as Gideon is freed from prison.
The entire car chase scene is an homage to the Mad Max film franchise.
One of Gideon's henchmen also resembles Max Rockatansky.
Soos describes Mabel's world as "shining, shimmering, splendid." This is a lyric from the song, "A Whole New World" from the movie Aladdin.
The scene where Mabel is napping in her tower resembles the film, Sleeping Beauty. Mabel's tower and bed are very similar to those in the film, and Mabel holds a rose while sleeping, referencing the iconic scene where Briar Rose is brought back to life by the prince.
While driving their car, Xyler and Craz briefly have their heads tilted back as they pass a shimmering rainbow-esque backdrop, referencing the Fabulous Secret Powers video by Slackcircus Studios.
Dippy Fresh's design is based off of Burger King Kids Club's Vid Kid.
During the end credits, Xyler and Craz reference the French philosopher Jean-Paul Sartre and his existential philosophy.
The song playing in the background when Gideon is dancing in his cage is Scott Joplin's "The Entertainer."
Bill mentioning the idiom "Achilles' heel" refers to Greek mythologywhere an immortal warrior named Achilles is killed when his heel is struck by an arrow.
Bill's story of coming from a "flat world with flat minds and flat ideas" is a reference to Edwin Abbott Abbott's novel, Flatland, about a two-dimensional world. In an AMA in April of the previous year, Bill stated that "EDWIN ABBOTT ABBOTT HAS A DECENT IDEA [about Bill's origin]."
Mrs. Valentino requesting the sawed-off shotgun in order to kill zombies is a reference to the Evil Dead franchise, because one of Ashley William's signature weapons is a double-barreled shotgun which he uses to kill the undead.
The "mermaid" that Soos holds up during the party, saying it is a monkey's body sewn to a fish, is a reference to the "Fiji Mermaid", a creature once thought to be real, but was determined to be a hoax.
The water tower's roar is the same as Bowser's from Mario Kart 64. 
Quentin Trembley is shown riding a horse backwards, much like Dudley Do-Right from Rocky & Bullwinkle.
Dipper's line "Ready to head into the unknown?" is a possible a reference to Over The Garden Wall, who's creator, Patrick McHale is a close friend of Alex Hirsch.
When the teens say "One of Us!" after Dipper and Mabel blow out the candles, it references to Freaks.
Dippers line in his ending monologue "It's not on any maps, and most people have never heard of it" is similar to a line from Herman Melville's novel, Moby Dick: "It is not down on any map; true places never are"