The fact Shaggy having an old ventriloquist dummy (named Harry) can allude back to the series that started it all where Shaggy was known to throw his voice in order to fool the villain.
Episode 8: "The Grasp of the Gnome"
The paramedics taking the frozen pirates to the Crytal Cove Mermaid Theatre looks suspiciously like John Gage and Roy DeSoto, if not actors Randolph Mantooth and Kevin Tighe who respectively played them.
The episode makes many references to Terminator: the robotic dog (Fright Hound) plays the role of the T-800, the Fright Hound survives the flames of an exploding car similar to how T-800 survived the flames of an exploding fuel truck, the Fright Hound’s disguise is burnt off at the police station, showing its endoskeleton underneath, which happens later in the movie, the climax takes place in a factory, even managing to bust down a factory door and after the robot is believed to been destroyed, it makes one final attempt before being crushed to death at the very end, the police station scenes... even the music is alluded to.
The machine Scooby uses in order to destroy the Fright Hound is very similar in design to the battle suit worn by Ripley to kill the Alien Queen in Aliens.
Episode 11: "The Secret Serum"
A character that looks like Cass Elliot appears in teaser amongst the audience at the auction.
The blond Don Knotts look-alike is seen during the charity auction as well.
The restaurant the gang visits in order to find a rare wine is called ‘Crab Net of Doctor Calimari.’ The oddly tilted windows are even a tribute to the movie’s setting.
Angie also mentions they having more vampire literature than anywhere "this of the Carpathian Mountainsnote The name of Dracula’s home at the beginning."
Where the gang suspects Daphne’s mother being a vampire is similar to an episode of Scooby-Doo & Scrappy-Doo called "I Left My Neck in San Franscisco" where the gang suspected Daphne might be a vampire when she keeps disappearing every time the vampire appeared.
The cursed ruby on display at Darrow University Museum of Oddities is called "the Devil’s Eye."
The leader Ernesto, who makes another appearance in "The Siren's Song", is based and modeled after Ernesto Che Guebara, the Argentine Marxist born Cuban revolutionist.
At the beginning of the episode, just before Char Gar Gothakon appears for the first time, there is an air freshener hanging from a rear view mirror shaped like Tweety Bird.
The numbers 4, 8, 15, 16, 23, 42 are written on a piece of paper inside the chest Mr. E sent the gang.
New management turning burger place "Burger Campus" into a Vegan restaurant is a nod to Casey Kasem, the original Shaggy, becoming vegetarian during the Scooby-Doo franchise run in the eighties.
Episode 13: "When the Cicada Calls"
Episode title alludes to Higurashi No Naku Koro Ninote Further evidence that the title is a reference is one of the main "mysteries" in Higurashi No Naku Koro Ni is where characters are driven insane. An example is one of the main protagonists, Rena the most notable character, investigates the disappearances and murders of people occurs on the same day in the past four years, figuring out all the disappearances and murders only happened to people who supported or worked on a discontinued dam project that would flood the small town they live in. These cases were also thought by the townspeople to be caused by the demon who apparently didn’t like the idea of the dam supposedly haunting the town. Along the way, Rena starts falling into insanity and at two points, starts shouting about there being maggots in her blood, frantically scratches and claws at her skin to get the "maggots" out.
Biologist Dr. Rick Yants bears a striking resemblance to Ben Ravencroft.
The teaser makes references to Gremlins where the pawn shop bears a strong resemblance to the antique store where Gizmo was bought and when Mai Le steals the ring, it has a creature that bears a strong resemblance to the pre-mutated Gremlins, specifically Gizmo, the original and only benevolent Gremlin.
Marcie "Hot Dog Water" Fleach’s father is named Winslow Fleach, now take off the "F" and ya got Winslow Leach.
Angel’s black cat-suit is very similar in design to the spy suits Sam, Alex and Clover wear when on missions.
Mr. E’s lair beneath Destroido HQ is very similar in design and appearance to Vector’s house.
When Angel first goes to talk with Mr. E, he is seated in a chair, watching several monitors to see what goes on, making it impossible for Angel and the audience to see who he is, is how Dr. Claw was portrayed.
Not only is the name of Angie Dinkley’s medium friend is "Lady Marmalade", the same title of classic song but the character quotes a lyric "Mocha chocolate, yaya", which she incorporated it as one of the coffee drinks.
Cass Elliot look-alike is seen attending a lecture by Regina Wentworth at Darrow University.
Regina Wentworth and her Dusk Teen Vampire Romance book is based on Stephenie Meyer and her Twilight Sagabooks .Twilight (2005), New Moon (2006), Eclipse (2007), Breaking Dawn (2008) and The Short Second Life of Bree Tanner (2010).
Obliteratrix’s exploding balls resemble similar weapons used by Red X.
Episode 26: "All Fear the Freak"
Episode's title refers to Blue Oyster Cult’s 1979 song "(Don't Fear) The Reaper".
After raking his nails across a chalkboard, episode’s villain makes a speech at the town hall meeting parodies the scene in which shark hunter Quint makes his first appearance:
Crybaby Clown: You all know me. You all know how I make a living. I'm a bad clown! Stopping me won't be easy... there's no string in the net to capture me as Mano Tiki Tia or Redbeard'sGhost! This Crybaby Clown swallowed your whole town, hahahahaha! You want your tourism back, you're going to pay me five million dollars! For that, you'll get the pacifier, the rattle, the whole darn clown! So, what's it going to be? Me or Mystery Incorporated?!
Fictional brand of pants promoted by Baylor Hotner is "Green Jeans," the name probably coming from fictional character Mr. Green Jeans.
The name of the fake bakery devised by Fred as part of the trap to capture Crybaby Clown is "Dawn ofthe Doughnuts".
Episode 28: "The House of the Nightmare Witch"
House of the Baba Yaga Witch coming to life and attacking people can allude to titular Monster House.
Episode 29: "The Night the Clown Cried II: Tears of Doom"
When the Hodag attacks the party and starts to grab people and drag them away, one of the guests tries to get away after being caught by crawling away but is only dragged back again into the shadows like how reporter Angela Vidal is dragged out of sight.
Traveling Cabinet of Curiosities owner's name, Gene Shepard, is based on Eugene Simeon Shepard, the original discoverer of the Hodag in Wisconsin.
Not only does Sheriff Stone accidentally solves a Lament configuration puzzle box, which clicks open and rearranges in a similar manner, but (after hearing a knock on the door) opening the door to his office to hear a disembodied voice manifestation which is a parody of the Cenobite leader Pinhead, before slamming the door and calling it a weirdo.
The disembodied voice saying "OH SUCH SIGHTS!" is like "We have such sights to show you!"
Inside the Cabinet of Curiosities, Jason Voorhees's hockey mask is seen.
Inversion of the usual standards for handsomeness suggests Twilight Zone episode "The Eye of the Beholder''."
The hillbillies from Scorpion Wells are based on the villainous clans of deformed cannibals from The Hills Have Eyes and its sequels as well as its remakes.
The crystal sarcophagus filled with black pears the Conquistadors found and later say is cursed is an allusion to the cursed Chest of Cortez in Pirates of the Caribbean: The Curse of the Black Pearl and the fact aformentioned sarcophagus is filled with black pearls alludes to the titular ship.
When the gang finds the soccer team’s lucky soccer ball, Boron had a hand print with a smiley face painted on it like Wilson the volleyball.
The title of Brad and Judy's semiautobiographical television series is Sternum to Sternum and parodies its opening theme.
In the yearbook, one student’s picture is named Scott Jeralds, a comic book artist responsible for drawing many Scooby-Doo comic books while another name appears is Vic Cook, the name of one of the show’s producers.
Mr. Peaches yelling out "Mr. Pe-Pe-Pe-Pe-Peaches" is like Brusier yelling out "Ba-Ba-Ba-Ba-Bananas" whenever he gets all excited.
When Scooby and the gang enter the main hall of Burlington Library, Dan Fluunk tells them the builder and owner of the mansion where they stand had a fascination with groups of four people and an animal who solved mysteries through the ages alludes to how in The League of Extraordinary Gentlemen, groups of different people that are real and fictional unite themselves in order to save the world throughout the ages.
When the gang finally find Abigail Gluck in her underwater robot factory, they turn the chair she’s sitting in only to find her corpse sitting there.
Tom, Tub and Scooby the Seal are from another Hanna-Barbera show called Moby Dick and Mighty Mightor, though unlike here where Moby Dick is a submarine shaped whale, he was an actual whale in the show.
Daphne mentions Tom and Tub’s parents are Dr. Paul Williams and Captain Michael Murphy, characters from another Hanna-Barbera show Sealab 2020.
Angel staying behind in order to keep the valves opened long enough for Moby Dick to get out of the underwater base is quite similar to Mitch Wilkinson staying behind in order to let Ben Gates and the rest of his group exit the cave in National Treasure: Book of Secrets.
Blue Falcon is depicted in the artistic style of Frank Miller’s Batman, even some lines of his dialogue are either direct quotes or homages owing to that work, such as the line about seventeen ways to incapacitate people, all of which hurt.
Even Dr. Zin, Jenny and their henchman Bobo also functions as Batman’s enemy Ra’s al Ghul, his daughter Talia al Ghul and Ubu, Ra’s al Ghul’s chief henchman.
The origins of Dynomutt becoming a cyborg because of a medical emergency is similar to those of Steve Austin and Jaime Sommers.
Not only do Race Bannon and Dr. Quest from the Quest team appear but so does Dr. Quest's enemy, Dr. Zin.
Velma's primitive recorder resembles the speak-n-spell phone-home transmitter used by the title character in ET The Extra Terrestrial.
Episode 41: "Theater of Doom"
After the original director quit directing the play about the loss of old Crystal Cove, Vincent Van Ghoul takes over.
On a wall of Angie Dinkley’s office is a poster with an UFO and the letters saying "Believe It," similar to what FBI Agent Fox Mulder has though with the words "I Want to Believe."
The Space Kook costume is stolen from the Crystal Cove Spook Museum.
Episode 43: "The Horrible Herd"
"Farmers Barrel of Crackerness," a bar for famers, is based on "Cracker Barrel," a famous chain of restaurants with a store attached.
The scene of Nova losing Scooby’s grip and falling from the helicopter and into the skull cattle’s stampede of the skull cattle is animated in a similar fashion to the scene from The Lion King where Scar pushed Mufasa off the cliff, into the path of wildebeests’ stampede, both victims mortally wounded. The only difference being Scooby tries to save Nova.
A villain’s scheme involving a mutated heard of cattle occurred in the predecessor series starring Scooby and the gangnote and by gang, we mean Shaggy. Velma, Daphne and Fred only had two to three appearances during the episode "Scooby Dudes''."
Episode 44: "Dance of the Undead"
The full first name used repeatedly by Scooby's parents is revealed over the hospital's intercom:
When Scooby and Shaggy ask Thorn, Dusk and Luna to help them break the spell from Rude Boys and the Ska-Tastics, the Hex Girls are each wearing their original outfits from their first aapearance. Also, their song "Who Do Voodoo?" is also featured.
The battle between the Hex Girls and the zombiefied Rude Boy and the Ska-Tastics where the music from their bands generates monsters that start fighting one another is reminiscent of a scene in Scott Pilgrim vs. The World, down to the victorious monster winning the music competition.
Professor Pericles says he managed to attach a mutated snake into Mr. E’s spine, thus making him more vulnerable mirroring a scene where Alex Krycek infects FBI Assistant Director Walter Skinner with some king of nanotechnology, making it impossible for his blood to receive oxygen when activated.
Not only do a big size Scooby and a big size Shaggy fighting the Gluten Demon is similar to Super Duper Sumos but is in a fashionable sumo wrestling style.
Episode 46: "Stand and Deliver"
The part where Scooby wakes up from the nightmare where he and Nova are attacked by Kriegstaffebots only to find himself in another disturbing dream before fully waking up is based on a similar dream sequence in An American Werewolf in London and Ghost.
Possibly unintentionally, the room seems strangely similar to Soul's mindscape from Soul Eater. Both are rooms visited mainly in a dreaming state by the individual, with primarily red and black decor, and a small man who is constantly dancing strangely. Furthermore, both are visited by their respective love interests while in the room.
Title of the episode is a reference to Adam and the Ants’ number one song in the United Kingdom about a "Dandy Highwayman," which happens to be the villain of the episode, who’s a homage to a homage to lead singer and chief songwriter Adam Ant.
Episode 47: "The Man in the Mirror"
Not only does the red room and the dancing reverb voice laden midget appears again from the previous episode but Scooby sees another version of Nova, just how Special Agent Dale Cooper sees another version of Laura Palmer whose murder he’s investigating along with the dwarf who apparently can talk backwards.
While the real Fred’s looking around post-apocalyptical Crystal Cove:
The Mystery Machine’s destruction is very similar to the Enterprise’s destruction down to the dialogue between Daphne and Fred being a near perfect recreation.
The underground attacker that attacks those by sound is how grabods attack victims who make noises.
After the denizens of Crystal defeat the Kriegstaffebots:
Stone: (to Mayor Nettles next to him) It’s not over yet, we have to get these people to safety! (stands on top the broken pile of bots) Listen up everybody! Follow me to FREEEDOOOOMM! (Crowd cheers) And will somebody please bring that sweet little dog in a coma? Thank you.
Episode 51: "Through the Curtain"
Not only are the four gate keys (the Primero Llave old flintlock pistol, the Segundo Llave a conquistador’s helmet, the Tercero Llave an old Mayan bow and the Cuarto Llave a torn piece of sailcloth) are tied to the four classical elements: fire, water, earth and wind/air respectively but with the Heart ofthe Jaguar, might be a reference to the five elemental rings bestowed upon Wheeler, Gi, Kwame, Linka and Ma-Ti, five youths of different diversities chosen to protect the Earth.
Probably unintentional, but given the themes pertaining to mystery solving groups, and the fact they follow a very specific 'same yet different' theme, retconning the whole series out of existence might remind some viewers of a certain videogame.