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  • Professor Emmanuel Rockelow is modeled after horror host, Mr. Lobo.
  • Velma does Phoenix Wright's "OBJECTION!" pose in episode 2.
  • The father in the Cold Open for episode 2 is obviously Clark Griswold.
  • In episode 4 two of the volleyball players look like the teenage Pebbles Flintstone and Bamm-Bamm Rubble. And the Cold Open features two teenagers named Dylan and Brenda. There are also two volleyball players that look a lot like Suzie and Anne Chan.
  • In the Ghost Rig episode, the Mystery Machine makes the same noise the Mach 5 makes when it uses its jump jacks.
  • The ghost rig itself is a reference to Steven Spielberg's early movie about a killer truck Duel down to the truck roaring like a monster.
  • The mayor refusing to close the volleyball court in episode 4 is very reminiscent of Jaws.
  • "Dance In My Pants" in episode 7 is a clear reference to Pants On The Ground.
  • One of the tourists in the episode 1 is obviously Don Knotts. He reappears again at the beginning of episode 9.
  • If the town of Crystal Cove is an allusion to Camp Crystal Lake, that Robot Chicken joint sketch has become Hilarious in Hindsight.
  • The way Shaggy is dragged off into the dark by the spookified children in episode 5 calls to mind the final scenes of REC and Quarantine.
  • Alice from episode 6 is a dead ringer for Spider-Man's own Gwen Stacy.
  • In the Cold Open of episode 6, Eric, Kitty and Red Foreman from That 70s Show.
  • Also in episode 6, Daphne's Asian counterpart, Suzie Chan from The Amazing Chan and The Chan Clan is seen walking the school hall in the background. She appears again in episode 16.
  • Vincent Van Ghoul's Lizard Face reveal in "In Fear of the Phantom" is a shout out to Vincent Price's unmasking in House of Wax.
  • Episode 7's villain in called "The Phantom", whose real name is Daniel, making for a subtle reference to Danny Phantom.
  • Fancy Pants is a reference too. Fairly Oddparents has a similar fallen musician who uses Sparky Pants and both Fairly Oddparents and Danny Phantom are created by Butch Hartman.
  • Episode 8 has a guy walking around that is an Expy of Candle Jack. And there are another two guys who bare a resemblance to Dirk the Daring.
  • Episode 9 is an extended homage to the classic Toho film War Of The Gargantuans, complete with the song "The Words get Stuck in My Throat". It also has slight references to The Incredible Hulk as there are two humongonauts, one green and one red said by the sheriff to be caused by gamma radaiation
  • Daphne's Hex Girls' outfit looks a lot like Starfire's.
  • Episode 10's monster is a robot double of Scooby, that at one point walks out of a large fire, without any skin. It then spends the rest of the episode trying to take out the gang. It's leitmotif is pretty much the main theme of Terminator as well.
  • The gang finally confront the Fright Hound in an abandoned factory, where Scooby takes it on with a forklift and a wink and a nod to another James Cameron film.
  • The main guard holds a grudge against a snapping turtle who bit his finger, paralleling Aaron Cash, who holds a grudge against Killer Croc for biting his hand off.
  • The gang finally meet Professor Pericles... who happens to be an inmate at an asylum for criminally insane animals.
  • When the gang go to visit Scooby at the animal asylum they are checked for weapons via a big walk-in X-ray device.
  • Near the end of episode 10, one of the animals being rounded up is a certain smarter-than-average bear.
  • The person behind episode 10's monster was Jason's Mom.
  • The name Jason Wyatt is likely a reference to the show's lead character designer Derrick Wyatt.
    • There's an actual Jason Wyatt who was the associate producer of that very episode.
  • Cass Elliot of the 60s pop group the Mamas And The Papas and guest star in season two of The New Scooby Doo Movies is among the patrons at the art auction.
  • Episode 11 has Velma's mom trying to order Sumatran Rat-Monkeys. Also The Crab Net of Dr. Calamari.
  • Episode 12, "The Shrieking Madness", is a big one to H.P. Lovecraft. The monster looks like Cthulhu, the title sounds Lovecraftian, there's even a deadring for the man himself, called Prof. H.P. Hatecraft, who writes horror books.
  • Hatecraft looks a little like he and Milton Dammers go to the same barber.
  • There's a student activist at the college who looks almost exactly like Che Guevara, he's even named Ernesto.
  • And near the beginning of "The Shrieking Madness", Fred's dad swears, "By Grabtharr's Hammer!"
  • A student in Velma's class has the name is Howard E. Robert like Conan the Barbarian creator Robert E. Howard.
  • The Numbers are on a page in the Darrow Family Files.
  • Hatecraft mentions Shuma-Gorath in one of his rants.
  • The 13th episode's title is a reference to the english translation to Higurashi no Naku Koro ni.
  • Episode 14's villain, Lord Infernicus, seems like a shout out and/or parody of fiery-headed villains, like Ragnaros and Dormammu.
  • Episode 15, "The Wild Brood", not only references The Wild Bunch and Lord of the Rings, we also get a shoutout to Swordfish.
  • The leader of the Wild Brood Orcs bare a resemblance to Thrall and Blizzard's particular brand of orcs.
  • Episode 16, "Where Walks Aphrodite", is not only a full episode reference to "Invasion of the Body Snatchers" especially the 1978 movie, we also get a nod to Stephen King's "Carrie."
  • Episode 17, "Escape From Mystery Manor", is a clear shout-out to the Saw franchise; the antagonist (an eighty year old man who happened to have been the last surviving Darrow) thought that Scooby and the others were the older Mystery Incorporated and set traps to prey on their weaknesses. He did apologize at the end because, well, he sort of lost track of time....just before running out of it.
  • Episode 18, "The Dragon's Secret", is not only an affectionate parody of Hong Kong cinema and the Pink Panther franchise, we even get to see a shout-out to Gremlins.
  • The tie-in game has Shaggy collecting books. One of them is called: I Have No Hand and I Must Clap.
  • Episode 19 is more or less a parody of the New Scooby Doo movies as well as a skewering of reality shows; also Vincent Van Ghoul shows up.
  • In Episode 20, Velma might as well use {=TrustNo1=} as her password; that's because she's channeling Fox Mulder and telling Angel or Cassidy or whatever her name is that she wants to believe.
  • The Season 2 opener is a whole episode Shout-Out to the other Hanna-Barbera mystery-solving teen shows, generating guest stars Jonathan Muddlemore, The Funky Phantom, Speed Buggy, Jabberjaw, and Captain Caveman.
    • The villain of the episode, Lord Infernicus/The Funky Phantom, could be seen as a third-rate impersonator of Dormammu (at least in terms of looks).
  • Episode 21 seems to be a tribute to the Bond franchise; that's because Mr E and Angel dress like they're five seconds away from telling Scooby that instead of expecting him to talk, they expect him to die. The man is in a supervillain lair, for pete's sake!
  • Episode 22 is a big, sloppy love letter to the Indiana Jones franchise; that's because Freddy gets to fawn over a muscle-bound archeologist who's an even bigger, jerkier adrenaline addict than he is. The character also deeply resembles Doc Savage. In that he is the exact opposite of him. Doc is highly educated, has a wealth of technology and near superhuman strength and endurence. Rick while he is high educated but is very stupid, he is very frail and headstrong and relies mostly on his partner to do the dirty work.
  • Part of Episode 23 seems to be a tribute to the Poltergeist movies; that's because Velma's mom gets a spirit medium friend of hers to scope out the "haunting" at Freddy's house. It doesn't go well.
  • Lady Marmalade, a character from episode 23, actually make a reference to a song of the same name.
  • Episode 24 is not only a tribute to westerns and police procedurals, we also get our first look at a man who's pretty much a composite of eighties television action heroes.
  • Episode 25 not only has a less than affectionate tribute to the Twilight series of novels, but Benton Quest and his friends appear in a cameo. It should also be noted that Oblivia's weaponry makes her more or less Girl Red X.
    • Also, the library at the college? The same one from Batman: Arkham Asylum.
    • In Hatecraft's home when he tries to get into the mind of a teenage girl, a poster of DC Comics character Prez is hanging on the wall
  • Episode 26 is pretty much a tribute to cliff-hanger season endings; not only is the gang in disarray and Pericles at large, we have Scooby pretty much setting up the Season 2 opener by going all Horatio Caine on us.
    • Scooby: I'll get the gang back together Pericles! We will find you, or my name isn't (puts on shades) SCOOBY-DOOBY-DOOOOOOO! (cue: YEEEAAAAAAAHHHH!!!)
  • Episode 27, a surprising one to Watchmen. When the masked trench coat person Velma is unmasked, she asks; "Who did you expect, Rorschach?"
  • The tie-in game gives a good one to the real Harlan Ellison's books. A Fetch Quest has you retrieving Ellison's books, one of which is "I Have No Hand and I Must Clap"
  • Sari Sumdac, another Derrick J. Wyatt designed character, makes an appearance as a background character in Season 2.
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