- Grimlock's sword and Lockdown's hook can be seen in Khyber's ship.
- In the Transformers Q&A Ask Vector Prime, it was explained that they had an offscreen crossover.
- Fistina is clearly based on Crasher from Challenge Of The Go Bots. In addition, her voice actress happens to be Morgan Lofting, who voiced a female Autobot named Moonracer in The Transformers. The GoBots were notorious for being a competitor with the Transformers franchise.
- On the street where the aliens play hockey in "Hot Stretch", you can see a truck with a red cab and grey container with blue and silver lines parked at the side.
- A Gavlan Recurring Extra resembles Sari Sumdac.
- The episode "It Was Them" is about giant rampaging ants.
- In "Predator and Prey," the alien Max is cooking looks like a facehugger. It even lunges at Ben's face!
- Malware's black and red design with a yellow spot may have been influenced by Panty & Stocking with Garterbelt.
- In the pilot there's graffiti reading "Reg Show" in the tunnels.
- "Many Happy Returns" a small girl Rath rescues from a fire, calls him "Kitty", might refer to Boo and Sulley from Monsters, Inc..
- There are three other Earth species on the Omnitrix: The first is humans, the second being dolphins.
- One of the signs in Bellwood resembles a yellow Slime.
- Since "Many Happy Returns", Gwen's wardrobe has gone right to the point where she resembles Velma Dinkley.
- "Blukic and Driba Go To Mr. Smoothy's" is a G-rated version of Harold & Kumar's first misadventure.
- As is tradition with Paradox, the words "Spoilers" and "Time War" crop up in "Ben Again." The Professor is also shown to have lost one hand just as the Tenth Doctor once did.
- Another reference to Doctor Who shows up in "Malgax Attacks." The device Azumuth made to disable the Omnitrix that he uses on the Ultimatrix looks exactly like 11's sonic screwdriver and has a similar function.
- Cow and Chicken appear as alien customers at a interdimensional Mr. Smoothy in "Store 23."
- Mr. Baumann is a Mr. Wilson expy. Five-year-old Ben even gets to say "MR. BAUUUUMAAAANN!" in the traditional Dennis voice.
- One of the aliens in "Special Delivery" is a parody of Thunder Cats. He also paraphrases Inigo Montoya's famous line.
- The predator counterpart to Humoungosaur is based on the Ultimasaurus from the Jurassic Park Chaos Effect toyline.
- The Incursean invaders from "Tummy Trouble" are from the Celebrated Calaveras Legion.
- Upchuck's feeling sick then stating that "Something's wrong...as if millions of stomachs cried out in hunger." is joke refering to Ben Kenobi sensing the destruction of Alderaan in A New Hope.
- The Upchuck's war cry of Alle Cusine is a reference to Iron Chef
- In "Frogs of War" Ben does the "boring conversation" bit from Star Wars when impersonating the Incursean Emperor. He even destroys the console like Han Solo did.
- Two aliens are a Shout-Out to Billy and his Dad from Billy & Mandy. They are even called Maxatomars and are said to be the funniest things in the universe.
- The Gentle Giant To'kustars are a shout out to the tokusatsu genre, in particular a certain toku star known as Ultraman. He has a Japanese accent in this series. Malware in particular evolves into something resembling Ultraman Belial.
- One of the mutant To'kustars that fights Ben looks like Scanty from Panty & Stocking with Garterbelt.
- In "Evil Encore", when one of the robot drones searches for Ben only to find him missing, it makes the ! sound from the Metal Gear Solid franchise.
- Ben says "Make like a tree and get out of here" when using his overboard in "Of Predators and Preys".
- In "Oh, Mother Where Art Thou?", Ma Vreedle threatens to launch a trilithium warhead at the sun if her son Pretty Boy is not returned. Her description of the weapon is practically lifted from the film, with a bit of flair thrown in.
- In "Arrested Developement", the robots from Dimension 12 resemble Omnidroids (Ben as Humungosaur even hurls a sewer lid at them!), but have the same Omnicidal Maniac motives as Daleks.
- The two aliens of Jury Rigg's species in "OTTO Motives" are clearly expies of the Car Talk hosts.
- In the same episode, Otto Gestalt is a reference to Power Rangers, and Kevin's Car!Upgrade is a reference to Transformers, which also doubles as a Production Throwback to Transformers: Animated. And they fight!
- Also in the same episode, Otto says "You knocked my block off."
- Ultimate Albedo heavily resembles the Marvel Comics villain M.O.D.O.K..
- Khyber's original pet is an Anubian Baskurr.
- In "Return to Forever", one of the robbers in the Cold Open (credited as "Tummy Face") is based on Krang in his robot body.
- In A Fistful of Brains, Ben, as Ditto, says "I knew we shouldn't have taken that left turn at Albequerque."
- One of the Vreedle Brothers gives a shoutout to Dirty Harry.
- In "Rad Dudesman" our heroes have to hire a space pilot, and later their ship gets dragged in by a bigger vessel belonging to an empire, but they stage a daring escape. Someone's even (temporarily) left behind. We even hear a Wilhelm Scream!
- Plumber communicators make the same sound as the ones in Star Trek: The Original Series.
- "Mystery, Incorporeal" is an obvious reference to Scooby-Doo! Mystery Incorporated. With Zed as Scooby, oddly enough. Complete with a door-chase gag. It makes sense since Derrick Wyatt worked on that show.
- Two hooded girls from the same episode resemble Jinx and Raven from Teen Titans (2003).
- The food truck on campus is called Miskatonic Madness.
- Gwen's new Anodite appearance is a palette swap of Marvel Girl.
- "American Benwolf in London" is an obvious reference to An American Werewolf in London. There's also Howl's Castle Moving and Storage.
- Dr. Jekyll was a Forever Knight, and created a formula to enhance the strength of the Knights using alien DNA.
- When Kai mentions Benwolf, Ben says that he doesn't call him that anymore. Kai asks what his new name is, and Ben looks over at a TV that's currently showing a news reporter, and comes up with the name "Blitzwolfer".
- When Ben, Rook, and Kai are in the graveyard, if you look in the background, you can see a Weeping Angel
- In front of Howl's Castle Moving and Storage, the Tardis can be seen.
- The episode is structured very much like an Indiana Jones movie.
- A couple of brief scenes that appear in "Rad Monster Party" while Ben is being chased by the townspeople, reference Rapunzel (with a mummy girl in the role of Rapunzel) and Frankenstein (with Ben as Frankenstein's monster and a Frankenstein girl as the little girl the monster throws in the river).
- Crujo is reference to the Stephen King novel Cujo, which is about a rabid dog.
- Crujo presents himself to Zs'skayr in a manner much like Darth Vader presenting himself to the Emperor.
- The twin Ectonurite girls in Zs'Skayr's castle saying "Come play with us" is a clear reference to The Shining.
- "The Vampire Stikes Back" is a reference to The Empire Strikes Back.
- In "And Then There Were None", No Watch!Ben senses he’s being followed and mutters, "Strange things are afoot at the Mr. Smoothy's…". This is doubly funny when you remember that Alex Winter directed both Ben 10: Race Against Time and Ben 10: Alien Swarm.
- In the episode "Catfight", one of Nyancy's cats looks like Oliver from Oliver & Company complete with matching back stripes and blue collar.
- The fish Rath catches in the underground river/sewer of Undertown, looks a lot like a giant Magikarp.
- In "Collect This", Collectimus is an obvious reference to Galactus.
- Ben's actor claims he performed a heart-wrenching rendition of Old Smeller.
- In "Blukic and Driba Go To Area 51", Benevelon says he is bringing 'peace' by way of violence. Ben as Four Arms calls him on this: "You keep on using that word. I do not think it means what you think it means."
- In "Weapon XI", Ben's malfunctioning Omnitrix makes the same noises as Al's link device on Quantum Leap.
- The episode's title itself is a reference to Weapon X, while simulatneously being a a pun on "eleven".
- In "Clyde Five", Driba eats a miniature Silkie.
- In "Rook Tales", during Max and Sheriff Wat-Senn's fishing contest, Max catches a Magikarp, and Watt-Senn catches a Gyarados.
- In "Charm School", the irate shopkeeper resembles a Shy Guy.
- Also, Jinx and Raven are both in Prof. Hex's class with Gwen.
- One of the alien artefacts in "Fight At The Museum" is a large, black monolith.
- There's also a row of shelves containing what look suspiciously like Cyberman heads as well as a Dalek.
- The episode title itself references the Night at the Museum series.
- The plot of "Breakpoint" is almost entirely a pastiche of Point Break (1991).
- The title of "The Color of Monkey" is a nod to the film The Color of Money.
- The shot of Ben's leg limping and then returning to walk normally is taken from The Usual Suspects
- When Buzzshock is attacking Suemongousaur (for a given value of "attack"), Ben's "Hoohoo-hoohoo-hoo-hoohoo!" is taken directly from Daffy Duck.
- "Stuck on You" features new character Skurd stealing from Ben's drink, exclaiming "I drink your smoothie. I drink it up!"
- After a fight with Maltruant in "It's a Mad, Mad Ben World Part 1", Ben and Ben 23 find themselves in a ruined city half-buried in sand. Amonst the stuff half-covered is Mr Smoothie. Ben's reaction?Ben: Oh no. They're maniacs! We blew up Bellwood! We blew it up!
- "From Hedorium to Eternity" features a visual nod to the iconic workers scene from Metropolis.
- "Secret of Dos Santos" has Kai reenact the famous pressure plate scene from Raiders of the Lost Ark. Ben screw it up by just grabbing the object before the switch.
- Charmcaster's dragon form in "Third Time's a Charm" is a blatant Maleficent reference.
- In Final Countdown, two recurring Plumbers are revealed to be named Bryk and Morty.
- Toepick is an ogre-like alien whose face is usually concealed by a metal cage. Anyone who sees his face is horrified, as in the old cartoon Mighty Man and Yukk, where big dog Yukk caused the same reaction when he removed the small doghouse that covered his head. In both cases, the audience never saw the characters' heads.
- "Malgax Attacks": Help me, Skurd the Slimebiote, you're my only hope.
- "The Most Dangerous Game Show": Charles Zenith answers to Prime-Time Lord Omega. That episode was written by Yuri Lowenthal, Ben's voice actor and a self confessed Whovian.
- The title itself is a nod to The Most Dangerous Game.
- In "The End of an Era" Future!Argit looks like Penguin from Batman Returns, or maybe even Control Freak.
- Can't believe no one's noticed that Feedback looks exactly like a Neoshadow from the Kingdom Hearts series, just with the gold things on his fingers and antennae.
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