In the first season finale, Webby remarks that if Millionara, the Villain of the Day, "offered me an apple in the forest, I sure wouldn't eat it!", and later Millionara says, "I'm glad I only packed the bare necessities!"
Cheerleading Instructor: This formation will make you stronger than a Geodude using its Harden attack!
Spinelli even appears in one episode as a background student with Kim Possible (Which is pretty funny for both of them, as Kim is in high school, not middle school, and had the Recess cast age in real time, Spinelli would've also been in high school by then)
It's slower than in the original The Court Jester, but in "Two Wheels, Full Throttle, No Brakes", Folsom and Fillmore reprise the "Get it?" "Got it." "Good." Running Gag.
James Bond isn't the only spy\special agent Kim has nods to. Her Kimmunicator ringtone, sound familiar? Used by a certain federal agent perhaps? And one episode has her don a black stealth suit, where at the end they are picked up by boat, who just happens to be driven by someone Kim refers to as Sam.
The Ren & Stimpy Show did this in at least one episode, where they used quotes from real kids' fan-mail saying how great Stimpy was, and viciously tearing into Ren. ("What is he anyway, some kind of mosquito?")
In "Off Balance", Batman asks Talia whose side she is on. "That would be telling" she replies. Almost every episode of The Prisoner started with that dialogue.
In "Nothing to Fear" the security guard in the beginning is reading a comic book called Tiny Toon Adventures. In a later episode, Bruce is discussing a ongoing case with Barbara Gordon. When he asks, "What are you doing tonight?" she replies, "The same thing we do every night, Pinky." He does not get the reference.
At the start of "Christmas With the Joker," the Joker is whistling the Looney Tunes theme.
In the same episode, he sings "Jingle Bells, Batman Smells" as he escapes Arkham.
The show has Adam West as part of it’s supporting cast.
In another episode, the inmates in Arkham are watching Bugs Bunny cartoons.
To It's the Great Pumpkin, Charlie Brown, where one thing Sally said to Linus in the pumpkin patch was, "If you try to hold my hand, I'll slug you!"; near the beginning of "Joker's Wild", in the lounge at Arkham Asylum, Joker cozies up next to Poison Ivy, and teasingly says, "If you hold my hand, I'll slug you!"
In the episode "Harley's Holiday", Harley Quinn, upon returning to Arkham, says the line, "Home again, home again, jiggity jig." It's a reference to the scene where one of the toys says the same line when J.F. Sebastian comes home with a woman in Blade Runner.
In episode "The Clock King", the streets have the names from various comics and animation artist who worked at Batman: Keith Weesner, Jack Schiff, Jerry Robinson, Norm Breygfole, Alex Toth, and Kurt Busiek.
The Freakazoid! episode "The Chip" has a couple of shout outs to one of the voice actors, Ricardo Montalban. The first is when he threatens to put "ooey gooey worms, that make you go all crazy" in the ears of Dexter and Roddy McStew. The second comes when he uses the phrase "Kirk, old friend..." before apparently realizing he was in the wrong character. Both gags come from Star Trek II.
In his second appearance, Guttierez gains powers like Freakazoid's, and is quite obviously Khan-inspired, with long white hair and rock-hard abs. Additionally, a Chekov-character appears in a TWOK era spacesuit.
In one episode, Brain and Wakko appear, after Freakazoid is called "wacko" for mowing someone's lawn. They are seen arguing over which show is Steven Speilberg's favorite. Wakko sings "Wakko's America" right after he appears!
Histeria! contained several nods to previous WB cartoons:
Big Fat Baby's jingle (the one where Father Time's chasing him in the desert) is based on the theme song from The Road Runner Show.
A song introducing a sketch about Alexander the Great is sung to the tune of the Animaniacs theme, and the sketch about Florence Nightingale as a Hospital Hottie ends with the boys shouting "Hello Nurse!" In a song about the Gold Rush, Father Time can be seen watching a TV with Yakko Warner on it. Also, the World's Oldest Woman's jingle is sung to the tune of Slappy Squirrel's theme, and Froggo's regular outfit is much like that of Wakko Warner (except that he actually wears pants).
The Pinky and the Brain theme music can be heard when Chit Chatterson mentions brain removal in a sketch about mummification, as well as part of the background music for the introduction to Nikola Tesla's later life.
Superman made three cameos himself, including one as William Clark.
Fetch bares a bit of resemblance to Hunter from Road Rovers.
In the World War II episode, Superman flies directly through a German plane and emerges from the inevitable explosion covered head to toe in flames - which makes him a dead ringer for the Marvel Universe's original, Nazi-fighting Human Torch. An unidentified Allied solider later in the episode is shown injured and clutching his eye in reference to Nick Fury.
In the same episode, the Flash heckles the Nazis by yelling "Over here, Colonel Klink!"
The Joker once also remarked to Batman in "Injustice For All" after Batman beat him up one more time "YOU'RE despicable!"
In the episode "Legends", part one, the giant robot at the beginning looks like it was commissioned by Gendo. The Justice Guild's sidekick "Ray Thompson" is an expy of Golden Age fanboy supreme Roy Thomas.
The exterior of Luthor's mansion, as seen in "The Return" looks quitefamiliar...◊
The JLU finale has Captain Steel channeling Captain America by flinging a Parademon's shield.
In "Eclipsed" Godfrey reads an anti-superhero diatribe from a book titled "Innocents Seduced." by "Dr. Fredrick" This is a riff on "The Seduction of the Innocent" by Dr. Fredrick Wertham, an infamous book about the negative effects of superhero comics on children.
The ending of "Panic in the Sky". An orbital laser weapon fails to do its job, then a few hours later a cocky git painfully transforms into a superpowered tentacle-monster. Why does this sound familiar?
When the Flash runs so fast he nearly enters the Speed Force in "Divided We Fall", the rapid montage of the world as he runs around it is reminiscent of Mike Jittlov's The Wizard of Speed and Time, another story about a speedster.
The giant, flying, turtle that attacks Japan in "Chaos at the Earth's Core" is both a Mythology Gag and a shout out to Gamera.
"Patriot Act" features Vigilante and Shining Knight discussing Dirty Harry.
In "Twilight", an incredibly powerful AI living in a space base has stumbled into the problem of having developed as far as computers allow, and must now merge with a humanoid alien in order to continue. In other words, same as the climax of Foundation and Earth.
In "Task Force X", when Deadshot meets Plastique, he says he's 'seen the pictures' to which she flirtatiously responds 'and that's as close as you're gonna get' - possibly reffing her naked humiliation at the hands of Firestorm in her first appearance.
In the episode "Divided we Fall," Green Arrow dissuades Superman from disbanding the Justice League, and gets ready to ride off into the sunset. Just before he does, Batman stops him, saying "Quis custodiet ipsos custodes?" To which, GA translates as "Who guards the guardians?" Most comic fans know what they're really talking about, though.
Another Watchmen reference appears in the episode "Paradise Lost," where we see Bernie's newsstand.
In Superman: Doomsday, there's a scene of Superman (actually his clone) fighting Toyman's giant mechanical spider. This was a shot at how movie producer Jon Peters wanted a giant spider in Superman Lives, written by Kevin Smith. Smith even voices a citizen in Doomsday that remarks, "Like we needed him to take care of a giant spider."
Although lots of shows poked fun at older video games of their respective eras, Tiny Toon Adventures brought out the hilariously direct Super Plucky-o Bros, featuring a side-scrolling landscape that all but matched the original game's colors and patterns, and sounds lifted straight from Super Mario Bros. 1 and 2.
The Parody EpisodeA Quack in the Quarks is one big shout out to Star Wars. "Duck Vader" is the Big Bad, and Buster ends up dressed like Han Solo, while Babs has her ears curled like Leia, and Plucky is dressed like Luke. It's not just Star Wars, though — if you look closely at the loading bay, you can see the TARDIS!
A scene of "Impact" has Toad knocking on the head of the petrified Mystique shouting "Hello? McFly?"
The Season 2 episode "Retreat" has a Bigfoot Watcher showing off his Bigfoot Caller to a buddy. He says what store you can get them in, and tells his friend to ask for Mulder. To cement the reference, a clip of The X-Files theme is played before the scene transition.
In Cruise Control, on a cruise ship in the Caribbean, Bobby is goofing off using his ice powers. His trump card is to make an iceberg in front of the ship, jumps right on the stern, and shouts "I'm king of the..."
In the episode "Uprising" when Spyke makes his return, Xavier uses Cerebro to find him. He says he's on the corner of "Lithia" and what sounds to be "Ashland" streets, a possible reference to the town of Ashland, Oregon: the town has lithium oxide (or "lithia") in a stream found in the center of town which is pumped into certain water fountains.
Scott and Kurt make a very dorky and completely out of place reference to Star Trek in an early episode. Justified though, as Kurt is a fan of fantasy in the comics and the Ultimate version of Scott is a Sci-Fi fan.
In "Walk on the Wild Side", the Bayville Sirens (X-Girls + Boom-Boom) do the "super-jiggle-sexy-slo-mo" walk down the hall a la The Craft, complete with Kitty blowing a kiss just like Nancy.
2 episodes had Kitty sleeping, no not like that you perverts, with a stuffed, supposedly purple, dragon, Not that Dragon, but a reference to Lockheed, Kitty's pet dragon from the comics & Ensemble Dark Horse.
Possibly why the latest group of superpowered teens is called the "runaways", including an episode title. They were more properly alien abductees and only ran away from League supervision.
Possibly unintentional, but the season finale of a two season super hero show involves the Heroes Unlimited cast coming together to break into teams and disable alien doomsday machines affecting the weather. Where have I seen that before?
Wally's Halloween costume in "Secrets" has the same letterman's jacket and pattern of hair as Teen Wolf.
In "Secrets", Miss Martian's "Martian" form is a slightly distorted Marvin the Martian with Godzilla's roar. The prankster that she is counter-pranking is even named Marvin.
When Miss Martian finds out that Billy is Captain Marvel, Kid Flash remarks "Yeah, and I'm Speedy Gonzalez."
In "Disordered", Superboy pilots the Super Robot Infinity-Man by docking his Super-Cycle on its head, just like how Kouji Kabuto pilots Mazinger Z with the Pilder. (The feature isn't in the Jack Kirby comics where Infinity-Man first appeared.)
In "Earthlings", Adam Strange quotes Lewis Carroll in order to get some Rannian policemen to chase him, specifically "Jabberwocky" and Alice in Wonderland. Later Alanna, who obviously has never heard this tale and does not speak English, tries to do this to Kroleteans:
In "True Colors", the Justice League logo that appears on Godfrey's show is identical to the logo for the DCAU series. Also the Green Beetle's name is B'arzz O'oomm, which when spoken sounds like Barsoom, the name for Mars in Edgar Rice Burroughs' John Carter of Mars series.
WB animated shorts are notorious for including crew names on background objects such as billboards or boxes. "Friz" shows up a lot, an homage to director Friz Freleng. In the short Rocket Squad, Porky and Daffy play future cops in a parody of Dragnet, and a list of "known criminals" they use to find the bad guy includes everyone working in the animation department at that time. A more complete listing of the various inside jokes can be found here.
In the short "Daffy Duck Slept Here", Daffy claims to be friends with a six-foot tall invisible kangaroo named "Hymie".
Another scene, where Optimus brandishes his swords before Megatron shoots him down is reminiscent of the duel between Indiana Jones and the Cairo swordsman in Raiders of the Lost Ark. Dinobot pushing Scorponok into his rotor blade weapon echoes the demise of the German engineer in the same movie.
Airazor's pose in "The Low Road" (as seen in the page image) is a direct reference to the famous Star Wars poster.
The sequence in Season 3 where Megatron is using the Transmetal Driver to create the new Dinobot II from a blank Protoform draws heavily from the classic film Frankenstein (1931).
In the episode "The Probe", the search and rescue probes sent out from Cybertron, shot for shot, mirror the imperial probe droids from the beginning of The Empire Strikes Back.
Several to classic Looney Tunes, mostly involving Waspinator getting scrapped.
The head writers involved were very active in the online fandom. As a result, these cropped up all the time, often in the form of locations. Subsector Hooks and Grid Joona, for example, are named after fans who posted on the alt.toys.transformers usenet group at the time.
At one point a concussed Waspinator refers to himself as "Wonko the Sane". While this was originally a name of a minor character in So Long and Thanks for All the Fish, the specific reference was evidently to another Beast Wars fan who used this name as an online alias. That fan, Benson Yee, went on to be recruited as a continuity consultant for the second season finale. The Beast Wars crew recognized the value of the fandom.
What may have been a very subtle Shout Out was Cheetor's weapon sound effect. It sounded just like Mega Man's from the cartoon. Both were voiced by Ian Corlett.
Rattrap and Optimus' dialog about the Ark, how "that ship wasn't built, it was poured" and "die-cast metal, its a lost art" are both about how the original Gen1 Transformer toys (well, the better, larger ones) all had die-cast parts for at least half the body.
Are we forgetting Megatron's first appearing to Optimus after he gets his new dragon body? "Enter the Dragon!"
Wreck-Gar, played by Weird Al Yankovic, yells at one point, "I dare to be stupid!" Which is the title of the song by Weird Al Yankovic that the original Wreck-Gar and the Autobots rocked out to for an indefinite period of of time in the original movie. The "Universal Greeting" associated with the song also gets a mention.
Wreck-Gar also bears a marked resemblance to his voice actor, even down to the facial hair. The whole thing gets topped off when, as he confronts Soundwave and tries to counter his music, he pulls out an Accordion.
The appearances of the human villains Angry Archer and Slo-Mo are based on Hasbro executives Aaron Archer and Samantha Lomow respectively. The former was unaware of the character until late in production, but his only request was that the Archer be left-handed so he was apparently not too upset about it.
Also Master Yoketron may have been named after Takara's lead designer on Transformers Hideaki Yoke.
Perceptor's voice bears a distinct resemblance to the synthesized voice of famous physics genius Stephen Hawking.
Highbrow is a clear shout out to actor Terry Thomas, from his accent to his "mustache" to the gap in his "teeth".
Rodimus' design takes the characteristics the original shared with Marvel Comics' Hawkeye and runs with them, even giving him a bow.
Not to mention Rodimus is voiced by Judd Nelson, his G1 version/counterpart's original voice actor in the 1986 movie.
Dirt Boss' design is extremely similar to another pint sized mind controlling villain, Marvel Comics' MODOK, and he's also a caricature of various real life mob bosses, particularly Al Capone, in temperament, speech, and methods, and later pulls a huge reference to White Heat; "Top of the world, cogs!" He's also the first legitimate homage to Tengen Toppa Gurren Lagann, his diminutive size being (especially the stubby legs) inspired by Lagann itself along with using drills to control other machines. And he looks sort of like Wario, to go with the Mario and Luigi-like pair of Scrapper and Mixmaster.
Huffer and Pipes take the Mario and Luigi thing to new heights, however.
The title "Decepticon Air" is a reference to the Nicholas Cage movie "Con Air", which also features prisoners being transported gone wrong. It help that the Decepticons are often called 'Cons for short.
Forsooth! It must not go unmentioned that, by Od's Beard, Ultra Magnus' hammer is strikingly similar to Mjolnir, possessed by the Odinson himself, Norse Mythology's Thor!
Lockdown wears a Western-style poncho in "A Fistful of Energon" for no apparent reason but to shout out to Fistful Of Dollars.
Flareup's accent is an obvious shoutout to how she was voiced in the Botcon script reading, "Bee in the City".
Plenty of incidentals are homages to characters from previous generations, such as Hot Shot, Red Alert (albeit gender-swapped), Strika, Blackout, Spittor... heck, characters like Powerglide, Beachcomber and Cosmos even show up in crowd shots on Cybertron!
Taken to extremes by the AllSpark Almanac, which manages shout outs to TF fandom memes, obscure characters (as in 'only appeared in a spin-off racing track set in 1984' obscure), and a metric ton of other stuff. That's not even getting into the non-Transformers stuff that gets namechecked. There's a map of the galaxy in the second Allspark Almanac featuring planets like Eternia, Krankor, and Marklar, among dozens of other refs on those two pages alone.
Even GoBots! Tonka was merged into Hasbro some time back, so they are now legally in the same universe after all. As such, Blackout's seismic stomp ability is said to have been based on technology from Gobots' Crasher, and Porter C. Powell's limo Stretch is patterned after the Renegade Tux. In fact, he's implied to be the very same character!
One of the mysterious Prisoners in Trypticon prison is Man bear Pig
In the Addendum at the back of the Collectors club issues has even more. Blot's chemical shells look like Metroids. And the Evil Sari of an Alternate universe has a sketchbook where she doodles a pony named RainbowDark.
In "Decepticon Air" Sari fixes the space bridge by extending her robotic fingers for quick typing. It looks exactly like similar scenes from Ghost in the Shell.
Sentinel Prime, voiced by Townsend Coleman, more famous for being the voice of The Tick. Sentinel Prime himself greatly resembles the character, being mainly blue, with a humongous chin and a head shaped like The Tick's mask. He even has a similar personality.
The Cool Shades worn by Prowl and Soundwave are a reference to the ones worn by the ABC Warriors of 2000 AD fame. (Although they also resemble those worn by Kamina, that's just a happy coincidence.)
Starscream's elaborate transformation in the season one finale harkens back to the stock footage transformations used in Transformers Armada and its sequels — although the Twinkle Smile smirk at the end just takes it on to parody. It does, however, bear exceptional resemblance to Gasket/Ransack's transformation from Galaxy Force/Cybertron. And Ransack's partner in crime, Crumplezone, probably wonders why Animated Bulkhead has his jaw. Furthermore, during Starscream's stock-footage transformation, he very obviously enters a state where most of him is still in jet mode, but his robot mode legs are folded below the jet. This "jet-with-legs" mode is a reference to the "GERWALK modes" that can sometimes be formed from Transformers with jet alt-modes. The term originally comes from Macross by way of the G1 Jetfire toy, (rather infamously) a recolored Macross Valkyrie, and has since been used in the fandom to describe similar "walking jet" unofficial modes.
Not even recolored - it's a simple repackaging of the Super Valkyrie set, and early versions came with the Macross logo painted on the wings.
In one of the shorts on the Season 1 DVD, one of Prime's fans asks him where his trailer goes when he transforms — a common question asked among fans of the original Optimus Prime. Optimus is confused, probably because he doesn't actually have a trailer. One of the kids kept trying to get him to turn into a fire truck. An actual episode would go on to have Blitzwing (while in crazy mode) say "Ooh, ooh, I wanna see him turn into a fire truck!"
Lately, Beast Wars references are all the rage: at the end of the episode that sees Wasp become Waspinator, he and Blackarachnia are teleported to a jungle, where a gorilla, a cheetah, a rhino, and a rat are standing over them, references to Optimus Primal, Cheetor, Rhinox, and Rattrap, the original four Maximals. Blackarachnia sees them, and says "You've got to be kidding." Also, a few episodes back, there was Tigatron Stadium. And earlier, during Sari's birthday party, the kids are hitting a pińata in the shape of a very familiar purple Tyrannosaurus. (You may also add the very existence of Waspy, Blackarachnia, and the more recently-introed Jetstorm, but that just comes with the TF franchise's oft-rebootedness.) Waspy is often showing parallels to the original, but being a darker and more tragic character than Beast Wars' resident Chew Toy, it's always got a sinister twist to it. "Waspinator has plans," indeed...
A sign that's a homage to the Sinclair Oil logo has a dinosaur that looks a lot like the Generation One Dinobot Sludge (who doesn't have a TFA incarnation).
There's also some self-reference lately: Bulkhead points out his susceptibility to The Worf Effect once. "I'll keep him distracted! He always shoots at me first." [Charges in, gets blasted all the way down the street by Blitzwing, flips over, and a pebble bounces off his head] "Called it."
Each member of Starscream's clone army has the color scheme of one of the Starscream-repaint Seekers from Generation 1.
They also get the names of those characters later on. The sole exception is Slipstream, since she was an entirely new color scheme for the mold as well as a girl.
Hanna-Barbera's The Adventures of Gulliver episode "The Dark Sleep". The witch Malagar was inspired by the Wicked Witch of the West in the 1939 film The Wizard of Oz.
She lives in a huge forbidding castle.
After she captures Gulliver, she holds up an hourglass and says "You have until the sand runs out, young Gulliver. Then, if you do not give up the map, I shall deal with you in my own fashion".
At one point she says "All in good time", a line spoken by the WWotW in the movie.
One episode had a gag involving a Swear Jar. It seems Francine keeps a separate labeled jar for each swear, and the one that was the fullest was labeled "Moist".
There are many shout outs in Arthur. There are shout outs to Chopin's Revolutionary etude, Invention 8 by J.S Bach, Child's Play — the movies, Death of a Salesman by Arthur Miller, Stellaluna, Jeopardy, James Bond, The Adventures of Tintin, Alice in Wonderland, Law and Order, Mondarin, Monty Python. This is still only about 4-5% of the shout outs from Arthur.
At the beginning of "Undercover", Ben is wary of Kevin testing the teleporter with a banana, questioning what would happen if a fly landed on the banana during the test, turning it into a "killer banana fly", a direct Shout-Out to The Fly.
The Boondocks has numerous Shout Outs to anime and manga, even in the opening credits of the first season, which are similar to the opening credits of Samurai Champloo. Jin also makes a brief cameo appearance. Another big Shout-Out is to Fist of the North Star at the very end of "Soul Plane 2: The Blackjacking", when Huey and Ruckus leap at each other, their outstretched legs crossing in midair. It's a reference to the first attacks Shin and Kenshiro make against each other when they finally fight.
"Nugget": There is a placard for "Mr. Warburton's Flim Flam Elixir"◊ in the background. It is a reference to the series creator Tom Warburton (who on this show is always credited as just "Mr. Warburton").
The Delightful Children are turned into sheep in one episode. The middle one resembles Sheep from Sheep in the Big City. Also, in "T.H.E.-F.L.Y.", one of the stuffed animals shown in Numbuh 3's room is Sheep.
In the episode "Frankie and Ellie Get Lost," Franklin behaving like Curly after drinking spiked punch (also resulting in him being the show's Cloud Cuckoolander), and has Albert Einstein acting like Larry and Ted Kennedy acting like Moe.
In the season 1 episode "A Little Deb Will Do Ya," Jay is about to do the deed with a woman he met at his sister Margo's debutante ball, but the woman admits to having a "terrible" secret below her waist. She's wearing the bottom half of the Humphrey the Hippo costume, also revealing to be his TV-ratings rival.
A reviewer's face melting off and reducing him to a skeleton (after Roger Ebert shows him a clip of a bad movie) is a reference to Raiders of the Lost Ark.
Speaking of "Reality Trip", the whole movie revolves around the villain Freakshow assembling magical gems to be placed into the Reality Gauntlet that, when complete, allows the bearer to rewrite reality at his whim. This is a huge reference to the Marvel story Infinity Gauntlet, only with Freakshow in place of Thanos, and three gems instead of five.
In "Public Enemies" when Danny fights overshadowed Kwan, the latter twirls a ghost guard's stick threateningly. Unimpressed, Danny just blasts him.
"What You Want" features the extremely popular (at least among Paulina and her cohorts) new movie "Sayonara Pussycat".
Ghost Rays in general look like the energy blasts from Dragon Ball, even the way Danny fires the extra-strong ones looks like a Kamehameha.
The chariot race in "King Tuck" is a reference to the famous scene in Ben Hur, complete with Messala's wheel-cutting spoke spikes.
There are also a few shout-outs to Back to the Future. Marty McFly himself appears in a brief, pause-or-you'll-miss-it cameo in "Masters of All Time" and "Splitting Images". George McFly's book "A Match Made in Space" is seen in "Double Cross My Heart". And the coolest; the clock tower in the University of Madison (in "Masters of All Time") reads 10:04.
There's an obvious nod in the episode "Lucky in Love" to Gone with the Wind. The Once per Episode title card was a parody of the famous movie poster of Rhett holding Scarlett in front of the burning city of Atlanta.
In "Mr. Right!", Timmy wishes that everything he says is correct. Including, at one point, "2+ 2=5".
Futurama had the Harlem Globetrotter planet, which was an extended shout-out to the old Hanna-BarberaHarlem Globetrotters cartoon series.
As well as the Globetrotters themselves.
In "Beast with a Billion Backs", when Bender assaults Yivo, the scene resembles a certain savvy pirate meeting a kraken with his sword.
Bender's guess about the nature of the god-like entity in "Godfellas", "the remains of a space probe that collided with God", is also a fairly accurate description of V'ger in Star Trek.
The episode "A Bicyclops Built for Two" contains several Shout Outs to Married... with Children, the show actress Katey Sagal (who voices Leela) was best known for before her work on Futurama. At one point, Leela does her hair up like Peggy Bundy, dresses like her, walks like her, and exchanges cheap dirty insults with her husband-to-be, an alien named Alkazar.
Turanga Leela: Aaaaaaaaal!
Two shout-outs to Star Trek in the episode "Why Must I Be a Crustacean in Love": The Decapodian tradition of dueling to the death is named Claw-plah (after the Klingon word for victory, Qapla'), and their national anthem is the dueling music often featured in similar deathmatches fought in the Original Series.
Another Star Trek shout-out that has already been used twice is the reference to Christopher Pike, former captain of the Enterprise, and particularly his wheelchair. The chair appears first in the episode "Love's Labours Lost in Space". Pike himself appears in the chair at Professor Farnsworth's 150's birthday in "A Clone of My Own". In both cases either the chair or pike's disfigured visage are subverted. The sliding doors used all throughout the show have the same sound effect from the ones in Star Trek, which is commented on by Fry in the first episode. He later gets stuck in the door too.
Even before Bender's Game, there were numerous shout outs to Dungeons & Dragons in the series, ranging from the obvious (Gary Gygax showing up in "Anthology of Interest") to the subtle (ranging from a rust monster at a veterinary hospital to a beholder in "How Hermes Requisitioned His Groove Back").
The Generator Rex episode "Breach" has Rex telling Holiday he was fighting a little girl, and she wasn't "made of sugar and spice!"
The entire episode (or at least Rex's segment) seemed to reference Silent Hill, foggy town filled with monsters, a creepy school, and the possibility of Alternate Dimensions being involved, not helped by some of the questions about Breach's psyche.
George's aunt(?) in George Shrinks tends to respond to shocks with "What in the name of (Insert Groucho Marx Character Here)..." - this has included such luminaries as Hugo Z. Hackenbush, Jeffrey Spaulding, and Rufus T. Firefly.
The episode Invasion from Below from the Hero Factory cartoon seems to be LEGO's take on Pacific Rim, which came out half a year prior. It has Kaiju attacking from a mysterious underground place, the Heroes riding mechs to fight them, the discovery that the beasts can communicate with each other, and one of the Heroes ejecting his escape pod upwards when his mech gets sucked into a chasm. Its animation studio Ghost VFX has also worked on Pacific Rim.
In the Inspector Gadget episode "Focus on Gadget", Gadget gets his nose caught in an airlock door, which is a callback to the closing sequence of Don Adams' earlier show, Get Smart.
Many of the structures in Republic City are shout-outs to easily recognizable real life architecture, such as the Golden Gate Bridge, the statues in the harbors of Hong Kong, Alcatraz, and the Empire State Building, and Avatar Aangs statue is green like Statue of Liberty. The city itself also bears a great resemblance to 1920s-era Shanghai and is similar in setting to many classic kung-fu action movies.
Asami's character design also seems a lot like a certain character from Fullmetal Alchemist (Bryan Konietzko did say that he watched FMA "after" designing Asami, but he did "borrow" Lust's lipstick color for her."
While not as Shout-Out-y as the current series, the original My Little Pony did have a few. For instance, on one occasion the Moochick and his rabbit assistant Habbit are seen playing three-dimensional chess. Amusingly, Habbit is winning.
One episode of Princess Gwenevere and the Jewel Riders opened with a bored fairy lamenting that her town was "boring" while her pet tried to talk her out of it. It was almost line-by-line taken from one of the best Adventures of the Galaxy Rangers episodes. Turns out that it was the same voice actress, and Jewel Riders used most of the same writers and staff as Galaxy Rangers!
In the Rocket Monkeys episode "Trick or Trixie", Gus is watching his pet space squid Inky make paintings on the wall out of ink. When Wally asks it to paint for him it shoots ink in his face that results in him looking like Gene Simmons, complete with hanging tongue.
One episode famously focuses on Jack's adventure with an obvious Totoro send-up. Later, Jack completely loses his memory because of Destiny's Child. Another episode has Jack fighting over a time traveling jewel with a palette-swappedDaisuke Jigen.
In the episode with the flatulent dragon. Jack gets directions from an eccentric scissor-smith, who tells him to turn left at a fork in the road to get to the Dragon's Lair. When Jack asks, "Where does the other path lead?" the scissor-smith replies, "Space Ace!"
Nearly any given SJ ep is going to have shout-outs. One ep had him encountering Quickdraw Mc Graw and Babalooie, as he's pursued by Old-West themed bounty hunters. In one where he fights an evil witch, she is voiced by BJ Ward, the VA for both Princess Allura and Witch Haggar on Voltron and is drawn like an SJ version of Haggar. She is even called The Hag.
Lest we forget about the episode "Jack's Sandals." Upbeat techno music? High-speed sneakers? Blurring by anything on feet or wheels? Sounds like a certain blue-quilled speedster we all know and love.
That one was also used in Weisman's other show Gargoyles episode "Future Tense", where Xanatos said the exact same thing.
While fighting a giant Sandman, Spider-Man cribs a line from Greg Weisman's time on W.I.T.C.H. regarding the similar villain Sandpit: "How am I supposed to beat up a beach?"
That's another one that goes all the way back to Gargoyles; after the heroes defeat a massive amount of sand controlled by the Archmage, he gloats that they accomplished nothing other than beating up a beach.
In the previous episode, Michaelangelo says, "Not today, Chung Lee." A triple entendre in that he references not only Wang Chung and Bruce Lee, but Chun Li.
In a fight, Donatello realizes, "A bo staff? And a bunch of guys who all look the same? Time to try one of my favorite movie stunts!" He spins around his staff Ă la Burly Brawl, but it doesn't work. Raphael (I think) reminds Donny that "This ain't the movies."
One episode has Donatello find wayward computer data in the systems of a Texas paper factory — likely a Shout-Out to Heroes, where The Company uses a paper factory in Texas as a front. Makes you wonder what other kind of data he'd find there if he looked...
In "Awesome" Spidey steals the Awesome Android from a SHIELD lab to pass off as his science fair invention. Among the items he passed on stealing are the Ultimate Nullifier ("too tiny"), the Cosmic Cube ("too bright"), and Howard the Duck ("too weird!").
2 Stupid Dogs once had a really weird episode where they were trained in using cartoon-violence. When they were asked to show some, very first thing they thought was to imitate The Little Mermaid.
In the X-Men: Evolution episode "Retreat", one of the Bigfoot hunters says that if you want the cool stuff at the cryptozoology supplies store, you should ask for Mulder. The BGM then plays the distinctive opening notes of The X-Files theme.