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    Season One 
  • "Tokyo Grows":
  • "Pinky and the Fog":
  • "The Third Mouse":
    • The episode is a parody of The Third Man, and also serves to give Brain another connection to Orson Welles.
    • When a female mouse asks Pinky what he knows, Pinky replies he knows all the words to "Yakko's World", while the "Mexican Hat Dance" plays in the background. This also doubles as an Actor Allusion since Rob Paulsen plays both Pinky and Yakko.
    • At one point, on the Ferris wheel, the Brain refers to the people down below as little dots, and Pinky remarks, "One of those dots is waving at us." Sure enough, Dot Warner is seen on the ground waving at the two mice.
  • "Meet John Brain":
    • Brain's entire run for president in this episode is based on real-life third party candidate Ross Perot, but in particular, Pinky's "Admiral Pinky" performance is based directly on Ross Perot's running mate, Admiral James Stockdale - the "Narf, ehehehe, what am I doing here?" is based on Stockdale opening the vice-presidential debate by (rhetorically) asking “Who am I? Why am I here?”, which was infamously mocked.

    Season Two 
  • "It's Only a Paper World":
    • The title is a reference to the song "It's Only a Paper Moon".
    • When trying to come up with schemes, Brain writes on the blackboard "KISS RULES".
    • Brain gets the inspiration for his next plan from watching a DIY show hosted by Martha Stewart .
    • One of the things Pinky impulsively buys at the megastore is an audiotape of Regis Philbin's autobiography I'm Only One Man!.
    • One of the newspapers used to make the paper-mâché world has the headline "BOFFO SMASH MAKES WARNERS CASH", referencing the Animaniacs song "Variety Speak".
    • Pinky's attempt at making a paper-mâché sphinx resembles Garfield.
    • The scene where Brain terraforms his new world with an ecosystem and vegetation, he decides to dub it "Chia Earth".
    • When Brain announces that Phase 3 of his plan involves a powerful force that makes man surrender to its every whim, Pinky thinks it's the Ark of the Covenant.
  • "A Little Off the Top":
  • "Brain's Song":
    • The title is based on that of Brian's Song.
    • As part of Brain's demonstration on the power of tearjerker movies, he subjects Pinky to a parody of Mufasa's death scene from The Lion King (1994).
  • "Welcome to the Jungle":
    • The title comes from the Guns N' Roses song of the same name.
    • The name of the Animal Wrongs Group, the Simian Liberation Army, is a reference to the Symbionese Liberation Army, a far-left terrorist organization best known for their kidnapping and brainwashing of heiress Patty Hearst.
  • "Two Mice and a Baby":
  • "Brinky":

    Season Three 
  • "Leave It to Beavers":
  • "Pinky and the Brain... and Larry":
    • Larry is based on Larry Fine of The Three Stooges.
    • At the end, Larry is replaced by a mouse named Zeppo.
    • Brain takes on the role of Moe by hitting Larry at every opportunity, at one point even getting a bit of wallpaper stuck to his head that looks like Moe's signature hairstyle.
  • "This Old Mouse":
    • The title is based on the 1979 television series This Old House.
    • In Pinky's vision of the future, Brian causes an avalanche by yodeling the tagline for Ricola cough drops ("Riiiiiiii-co-laaaaaaa!!!").
  • "Brain Acres":
  • "A Pinky and the Brain Halloween":
    • One of the trick-or-treaters seen in the beginning is dressed as Fred Flintstone. Three kids are dressed up as Yakko, Wakko and Dot. Three others can be seen dressed as a lion, a witch and a wardrobe.
    • When Brain throws a piece of candy at Pinky, causing chocolate to splatter on Brain's Jack-o-Lantronic Transmitter, their exchange is based an old advertising campaign for Reese's Peanut Butter Cups ("No! Pinky, you got chocolate on my Jack-o-Lantronic Transmitter!" "You got Jack-o-Lantronic Transmitter on my chocolate! Yummy!").
    • The name "Mr. Itch" is based on one of many euphemisms for The Devil, "Old Scratch".
    • The rhythmic gymnastics tournament is held at Mile Down Stadium, which is a parody of Mile High Stadium.
  • "Inherit the Wheeze":

    Season Four 
  • "Brainwashed, Part One: Brain, Brain Go Away":
    • The singing group BAAB is based on ABBA.
    • When Pinky says that the lab was destroyed by "the clown from Washington, D.C.", Brain guesses Newt Gingrich.
    • The Land of Hats, complete with its naming scheme, parodies The Prisoner.
    • The scene where the residents of the Land of Hats point at Pinky while making inhuman screeches parodies Invasion of the Body Snatchers.
  • "Star Warners":
    • The episode is a spoof of the original Star Wars trilogy.
    • The name of the spaceport town is Moe Eisner, referencing the then-CEO of The Walt Disney Company.
    • Slappy Wanna-Nappy tries to sell a TV pilot called I Love Slappy.
    • Alien versions of The Jetsons are watching TV when Girth Plotz's Mega Star satellite jams the TV signals with infomercials.
    • Slappy says she was watching Scooby-Doo when her TV signal was jammed.
    • The Cantina Scene contains several appearances from characters from other Warner Bros. cartoons (such as Freakazoid, Fanboy and Mo-Ron as the house band, and The MonStars and Duck Dodgers as patrons), as well as one of the Street Sharks.

    Comics 
  • In "Brinky 1/2", there's a reference to Ranma ½. Pinky and Brain head to China and fall into the "Spring of the Drowned Martial Arts Master With a Split Personality", which merges them into one mouse - hot water switches them to Pinky, and cold water switches them to Brain. The story ends with them falling into a bowl of Hot & Sour soup and splitting back to normal due to the 'contradictory nature of the soup'.
  • In the Christmas special, Pinky and Brain get trapped in packaging for Mighty Tidy Rodent Rangers.
  • In "Brain Pan", Brain's newest invention causes him and Pinky to occasionally turn into Brain Pan and Pinkerbell, respectively.
  • In the first issue, the duo browse comic books such as Squirrel-verine (who references Alvin and the Chipmunks), Fawn (who also references Bambi), Le Facial Masque and Bughead (who looks like Jughead crossed with a Xenomorph). In addition, their costumes resemble Batman and Robin (they even have a Bat-Cave equivalent, while Brain's evil counterpart has a hideout named the Fortress of Fortitude), and they meet a brunette masked version of Wonder Woman.
  • Brain is dressed like Elvis Presley on the cover of the second issue, and a long-haired version of the Disney version of the young King Arthur appears in the last three panels of the first story.
  • In Issue 3, Pinky protests that altering time should only be done by professionals like Michael J. Fox or Doctor Who, and a Batman action figure can be seen in the following panel.
  • The cover of Issue 4 depicts Pinky as Dorothy Gale and Brain (ironically) as the Scarecrow.
    • At the start of the story, Pinky mistakenly thinks that a Mickey Mouse hat is the scalped head of an actual mouse.
  • Brain's plan in Issue 6 involves making a movie that parodies Plan 9 from Outer Space, and includes references to the production (e.g. replacing actors with ones who look nothing like the originals).
  • In Issue 7, Brain-as-Faust gets the idea to make a Deal with the Devil when he sees his friend Dorian Greymouse is still young despite being much older than Faust. Also, Mephistopheles pulls the Energizer Bunny out of a hat.
  • The stories in Issue 8 are called "Mission Inpinkable" and "I, Brainius".
  • The first story in Issue 9 is called "The Mouse Who Would Be King".
    • There are several references to the Book of Exodus - Pinky and Brain make their appearance in the story by floating down the river in a basket, a la Moses; two of the three "miracles" Brain performs to prove that he is a deceased Pharoah are turning the Nile blood-red, and unleashing a plague of locusts, and Moses and the Israelites can be seen at the end when Pinky and the Brain are banished from Egypt.
  • Issue 10 parodies Mad Max.
  • The first story of Issue 11 is called "Narftasia", and parodies the Sorcerer's Apprentice section of the film (with the other segments making cameo appearances).
    • Batman makes a cameo as a giant bat Pinky needs a nose hair from.
    • The second story parodies Sherlock Holmes - specifically, "The Final Problem".
  • The second story in Issue 12 is called "Moby Dinky", and Brain spends most of the story with a spittoon on his foot, making him resemble Captain Ahab.
  • "Ali Brain and the Forty Thieves" parodies Ali Baba for the most part, but the magic lamp is from Aladdin.
  • The first story of Issue 14 is called "Brainlet".
  • Officer Marge Gunderson appears in the fifteenth issue in pursuit of a criminal.
  • The first story from Issue 17 is called "Pinkenstein", and parodies the movie version.
  • In "Braintech", Brain turns Acme Labs into the Battleship Acme-moto.
  • In "Anti-Claus", Pinky hires the Penguin's rocketeer penguins to help him and Brain make toys.
    • The lawyer who sues Pinky and Brain is named Virgina.
  • The first story of Issue 20 is called "Mice in Pink", and Pinky sings a version of the theme song from the movie with altered lyrics.
    • During the song, random "factoids" a la Pop-Up Video appear.
    • The alien leader makes numerous references to disco songs, like "Disco Inferno" and "Funky Town".
    • The second story is called "Brainberry R.F.D".
  • A blue version of the Yellow Submarine appears in "Fantastic Voyage to the Bottom of the President's Brain".
  • "The Mouse in the Iron Mask" references The Man in the Iron Mask.
  • The ending of "Stunted Publicity" ends with Pinky and Brain disguising themselves as female musicians in order to escape the people out to get them, a la Some Like It Hot.
  • The cover of Issue 23 references Jaws.
    • The second story is set in Oz.
    • Pinky and Brain reference The Beach Boys songs "California Girls" and "Good Vibrations".
    • The Gnome king makes a cameo.
  • In the first story of Issue 24, Brain poses as "El Cerebro".
  • In Issue 25, Pinky and Brain once again become Expies of Batman and Robin, and initially speak like the Adam West and Burt Ward versions of the characters. Billie also appears as Poison Billie.
    • The giant T-Rex statue that appears in the duo's basement resembles a purple version of Rex.
  • The first story of Issue 26 parodies The Scarlet Letter when Brain is forced to wear a red lettuce on his head.
  • The first story of the final issue is called "Were-Mice of London".
  • From the Animaniacs comics:
    • Pinky and Brain are dressed as Wilma and Fred Flintstone, respectively, on the front cover of Issue 3. Fred and Barney also make a cameo appearance in their story.
      • Rickee Rat makes a brief appearance in the third-from-last panel.
    • The Pinky and the Brain story in Issue 9 is called Reservoir Mice. In addition, Pinky, Brain and the three mice they hire to help them wear the suits and sunglasses from the movie, and adopt the same colour themed codenames (except Brain).
    • In Issue 12, Pinky and the Brain meet No Celebrities Were Harmed versions of The Beatles, and both mice mention several titles of songs by the Fab Four.
    • In Issue 19, Pinky and Brain disguise themselves as Fox Mulder and Dana Scully.
    • In Issue 28:
      • Brain poses as Mr. Spock as part of his latest plan, and several other Star Trek references are made.
      • Brain suggests that Pinky pose as a Wookie.
      • Brain accidentally makes the scientists suspicious by saying "Nanu Nanu!".
      • Brain expresses a fondness for Xena: Warrior Princess.
      • Pinky initially thinks that Brain has disguised himself as a Keebler Elf.
    • In Issue 37, Brain hosts a children show based on Mister Rogers' Neighborhood.
    • In Issue 49, Pinky pretends to be Xena: Warrior Princess while playing with Brain's sword.
    • In Issue 51, Pinky compares Brain's plan to one from Batman Beyond.
    • In Issue 54, Pinky sings the chorus to "I've Been Working on the Railroad".
    • The story in Issue 56 is titled "The Britches of Madison County".

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