The ending song jokingly and mockingly references Black Mesa. Songwriter Jonathan Coulton also namedrops another of his popular songs, "I Feel Fantastic".Black Mesa is also referenced in several slide shows left running in staff areas that are accessible or at least you can see into easily.
Doug Rattmann's den in the Companion Cube level also contains a rather well-hidden shout out to Isaac Asimov's short story "Escape". His dens all have some poems altered to include cubes and the like. Here is a full list of the graffiti drawings.
Delicious and moist" cake was originally a joke in Psychonauts.
In the testing room for military androids, GLaDOS's dialogue implies that robots and androids are programmed with a belief in "Android Hell" in order to ensure their compliance. This shouts out to Red Dwarf, wherein robots and androids are programmed with a similar belief in "Android Heaven" for a similar purpose.
At a party where Ray and Winston were performing, when they asked Who You Gonna Call?, the kids answered "He-Man".
The title is a parody of the first line of The Christmas Song, "Chestnuts roasting on an open fire...
Bart mentions Charlie Brown, Tiny Tim, and The Smurfs.
Two of the incorrect names for Santa's reindeer Homer says are Nixon and Donna Dixon.
Maggie spells E = MC Squared with blocks.
The family goes to see Carmen.
The title is a pun on the Greek poem The Odyssey by Homer.
The title is a pun on the line "There's no place like home" from The Wizard of Oz.
Burn's Manor, as always, resembles Kane's mansion from Citizen Kane.
Bart claims one of the only good wars to be the Star Wars trilogy.
The training montages parody Patton (specifically the music) and Full Metal Jacket. Grandpa even refers to Gen. George S. Patton by name.
At one point Homer does the Tarzan yell.
The title and plot are based off the story The Telltale Heart.
When Aput tells Homer that he looks familiar (due to seeing him on the incriminating photo), Homer believes he's confused him for Fred Flintstone.
During the bachelor party the guys sing "Barnacle Bill the Sailor."
The title is a pun on the novel The Grapes of Wrath.
Scooby-Doo, Where Are You!: When Sideshow Bob is arrested, he admits his crime and that he intended to frame Krusty, exclaiming, "I would have gotten away with it, too, if it weren't for You Meddling Kids," referring to the common ending line of most episodes where the Mystery Inc. kids foil criminal activity.
The people of Springfield stand and sing in a circle, as in the ending of How the Grinch Stole Christmas!.
Bart says that the first Friday the 13th movie is tame compared to later films in the series.
Bart and Tom watch an episode of The Ren & Stimpy Show.
Homer imitates the final scene of Planet of the Apes when he finally gets the film's twist.
One episode has Johnny turned into a mouse, and the villain is a cat. Predictability ensues.One of the early episodes had a toy series called Roboticles. Coincidentally, Johnny's voice actor would later voice a character in the actual series, while some of the other voice actors have already been in other BIONICLE movies.At the end of "Johnny vs. Bling Bling 3", Johnny steals a page from John McClane's book (specifically, "surrendering" with a weapon taped behind him).One one-off NPC is wearing Luigi's hat."Whatcha doooin'?"The sleepover episode turns into a Cat in the Hat homage halfway through, with Bling 1 and Bling 2 running around with kites, a talking fish, and Dr. Seuss dialogue and gadget designs.In Johnny of the Deep, Bling Bling loses a ring that hypnotizes Susan into falling in love with him. When it falls overboard, he says "it was the rarest of gems."The episode where Bling-Bling gets his mission to destroy Johnny ends up as a Road Runner reference, complete with Canis Latinicus scientific names for the character."Johnny Dukey Doo"In one episode, Johnny gets a brown, bushy mustache; when questioned about his name, what does he say it is?Earl.Hi-Pitch Hal"Johnny Test's Quest" not only was the episode a direct reference to Johnny Quest (Including Mr.White dressing up in Hindi clothing.) but wouldn't be surprising if the episode was only made as an in-joke because the names sound similar.
When the moonfish form the shape of a sailing ship, they start singing "Got a whale of a tale to tell you, lads..."
"Swiiim awaaay!". Also several others.Speaking of Monty Python, there's an added joke about a character named Bruce having an Australian accent.
Bruce was the nickname Spielberg gave the animatronic shark, though not the name of the shark itself.And the torpedo sliding into his mouth is reminiscent of the shark in Jaws with the air tank in his mouth
The Psycho Strings and the gulls surrounding Nigel, Dory and Marlin like a certain scene in The Birds...and it's been said Pixar don't reference other movies!
There's also P. Sherman's address, 42 Wallaby Way.
In the dentist's waiting room, a Buzz Lightyear doll can be seen on the floor, and a boy is reading a Mr. Incredible comic book.