- The opening sequence with the reverberating red circles is a reference to the 1950s Blob film.
- On a related note, the opening alone is a callback to the theme song from the series the older generation grewed up with
- Mark Hamill and Trickster appear in back to back episodes, with both of them referencing The Joker, in Hamill's case, he accidentally cracked a Joker laugh after mentioning the Batman episode and Trickster wore a Joker mask under his monster mask and did a Joker impersonation. All three of them appeared together in a Justice League Action web short where Hamill did impersonations of the two others.
Episode 1: "Revenge of the Swamp Monster!"
- While trying to pretend he was an art teacher to The Swamp Monster, one of Chris Paul's quotes was "We don't make mistakes, only happy accidents."
- Another well-known came from Shaggy
- The Running Gag where Scooby-Doo is being teased by two gophers, may be a reference to Caddyshack, as both this and the episode takes place on a golf course.
Episode 2: "A Mystery-Solving Gang Divided!"
- Fred says, "We'll head 'em off at the pass!" to which Daphne replies, "I hate that cliché!
Episode 3: "Peebles' Pet Shop of Terrible Terrors!"
- Shaggy is bitten by a bulldog that looks just like Bandit from Jonny Quest.
- Magilla Gorilla forming a friendship with the kitten Mr. Jones is a reference to Koko the gorilla.
Episode 4: "Elementary, My Dear Shaggy!"
- The episode's title is a reference to Sherlock's iconic catchphrase: "Elementary, My Dear Watson."
- The laugh sound from The Screaming Skulls is incredibly identical to that of the Spooky Space Kook from "Scooby-Doo, Where Are You!"
Episode 5: "Ollie Ollie In-Come Free!"
Episode 6: "The Scooby of a Thousand Faces!"
- Scooby and Shaggy run away from a giant concrete rolling ball. Where have we seen that before?
Episode 7: "The Cursed Cabinet of Professor Madds Markson!"
- The scene where The Mystery Gang, Penn and Tess Flemming all escape out of the Savannath Hotel before it burst up in flames is a callback to McClane's escape.
- In one scene Teller pulled off a trick with cardboard cutouts on a model train set
Episode 8: "When Urkel-Bots Go Bad!"
- The episode featuring Steve Urkel has him frequently earn the ire of a loud-mouthed, overweight man with a mustache, and having to deal with evil robots. There is even Sonic's "juicing/revving" sound effect heard when Urkel reactivates his robot made in his own image. Steve's voice and inflections are even used for Princess Sonia Hedgehog, Sonic's sister in Sonic Underground. Sound and feel familiar?
Episode 9: "The Fastest Fast Food Fiend!"
- The Spectral Speedster has a design that resembles Rat Fink's
Episode 10: "Attack of the Weird Al-losaurus!"
- Several to Jurassic Park
- The Allosaurus has the same roar as the Tyrannosaurus rex from the films.
- Scooby, Shaggy, and Weird Al attempt to hide from the Allosaurus by standing very still, under the assumption it cannot see movement. It doesn't work, though.
- The Allosaurus chases after the Mystery Machine, complete with Shaggy urging Fred to go faster and a rear-view mirror shot.
- The villain of the episodes are a pair of Allosaurus, a reference to one of Weird Al's songs: "Jurassic Park" which is a mix of MacArthur park and......well, it's pretty obvious
- A nonJurassic Park example would the culprits: Pete and Pete, who are a a pair of twins with the same name.
Episode 11: "Now You Sia, Now You Don't!"
Episode 12: "Quit Clowning!"
- Inside the TV station, framed pictures of "The Banana Splits" and "The Herculoids" are seen in the backgrounds.
- When Pazzo the Ghost Clown captured what he thought was Fred and Daphne but they turned out to be a pair of mannequins. The real Fred and Daphne managed to sneak out dressed up as Fred Flintstone and Jeannie. No, not the Barbara Eden character most of us are familiar with, but the one voiced by Julie McWhirter.
- The old Pazzo the Clown show is an Expy of Bozo the Clown.
Episode 13: "What a Night for a Dark Night!"
Episode 14: "The Nightmare Ghost of Psychic U!"
Episode 15: "The Sword, the Fox, and the Scooby-Doo!"
- Several to "Star Wars" from Shaggy and Scooby-Doo using fish as Lightsabers to one of the trashcans in the backgrounds looking like R2D2, likely due to the fact that Luke Skywalker is the guest of the day in the episode.
- Another one to Star Wars is the various photographs Shaggy keeps having Mark sign. They are all done to look like paintings, just like the classic movie posters for the franchise before Disney acquired it.
- The fur pattern on the fox monster is reminiscent of the eponymous creature from My Neighbor Totoro.
- The first attempt to capture the fox monster is a reference to the Japanese story of Kiyohime.
Episode 16: "One Minute Mysteries!"
- The title is a reference to Donald J. Sobol's Two-Minute Mysteries books.
- The Flash pulling Daphne, Velma, and Fred out of the exploding toy factory at high speed is reminiscent of a similar scene involving rival speedster Quicksilver from X-Men: Apocalypse.
Episode 17: "Hollywood Knights!"
- In one scene we get a glimpse at George Takei's house, which looks exactly like the Starship Enterprise.
- For the Scooby-Dooby Doors sequence, the gang plays the Keystone Kops.
- In a reference to a very specific episode of Star Trek: The Original Series, George Takei wields a fencing sabre while shirtless, and mentioning Richelieu.
- In a reference to ST:TOS episode, "Return of the Archons", Mystery Inc. first show up cloaked in brown hooded robes.
- George Takei tells Fred to drive faster. Fred replies,"She'll shake apart!" George replies, "Shake her apart, then!"
Episode 18: "The New York Underground!"
- The Scooby-Dooby Doors scene includes a reference to the Teenage Mutant Ninja Turtles. At some point in this scene, which is set in the sewers, the Gator Man Monster is seen running away from Mystery Inc. and Halsey, who are all wearing red ninja headbands. Scooby, Halsey, Velma, and Fred are wielding a nunchaku, a pair of katana, a pair of sai, and a bō respectively, while Shaggy uses a skateboard and is eating a slice of pizza, all of which are trademarks of the Ninja Turtles.
Episode 19: "Fear of the Fire Beast!"
Episode 20: "Too Many Dummies!"
- The gang stays at a creepy motel with a mansion in the background that looks suspiciously like the Bates house.
- The evil dummy is designed to look like The Joker, and seems to be channeling Paul Lynde for his voice.
Episode 21: "Dance Matron of Mayhem!"
Episode 22: "The Wedding Witch of Wainsly Hall!"
Episode 23: "A Run Cycle Through Time!"
- When Scooby-Doo and Shaggy spotted a Giant Banana in the future, they say the following:Shaggy: Come on, Scoob, I think it's time we went-
Episode 24: "I Put a Hex on You!"
- The episode title likely refers to the song "I Put a Spell on You" (particularly as performed by another female trio).
- When Thorn greets the delivery man, she says, "Welcome to our nightmare," a reference to Alice Cooper.
- Thorn's bat necklace was redesigned slightly to resemble the red bat emblem from Batman Beyond.
- When trying to stall for time, Scooby Doo goes out on stage and says "Hello, Cleveland!"
Episode 25: "The High School Wolfmans Musical Lament!"
- While more of a Take That! than a Shout-Out, during the song "Diners for Dinner, Dinner for Diners". "Christian Slater" says "I love hearing a dog talk, and you know i don't mean Scrappy."
- The dance Velma does in the final song is a homage to "Red Hot Riding Hood"
Episode 26: "Space Station Scooby!"
Episode 1: The Phantom, the Talking Dog and the Hot, Hot, Hot Sauce
Episode 2: The Last Inmate
Episode 3: The Horrible Haunted Hospital of Dr. Phineas Phrag
Episode 4: The Hot Hot Dog
Episode 5: A Movable Mystery
Episode 6: The Feast of Dr. Frankenfooder
Episode 7: A Fashion Nightmare
Episode 8: Scooby on Ice
Episode 9: Caveman on the Half-pipe
Episode 10: The Crown Jewel of Boxing
Episode 11: The Internet on Haunted House Hill
Episode 12: The 7th Inning Scare
Episode 13: The Dreaded Remake of Jekyll and Hyde
- Sandy Duncan, in her second encounter with Scooby-Doo, is starring in a Jekyll and Hyde movie, as she did the first time.