Impossibly Cool Clothes: Averted by Fred's team uniforms in episode 9. Fred's the only one who thinks they look any good.
Ink-Suit Actor: Professor Pericles, despite being a parrot, bears a slight resemblance to his voice actor Udo Kier, especially the forehead.
Horatio Kharon resembles his actor, Michael J. Anderson, furthering the fact that he's a recreation of a particular Twin Peaks character.
In Medias Res: "Howl of the Fright Hound" begins at the climatic action.
Indy Escape: Episode 22. A rolling idol head nearly runs over a Damsel in Distress. Subverted because she set up the whole fake temple and knew what to expect, and her leg was not injured as she pretended.
Innocuously Important Episode: Episode 2 of Season 1, "The Creeping Creatures", was more or less a self-contained episode, not really related to the mystery of Crystal Cove. "Theater Of The Doomed", however, has the ghost of Friar Gabriello repeat the words of the Signs of Disrepair ("The Dog Dies") from that episode.
In Spite of a Nail: The altered timeline at the end of the series has a lot of examples. Notably, Fred still got the name "Fred" despite him presumably having been named after his fake father, who in this timeline never kidnapped him and raised him.
Irony: Scooby and Shaggy, the scaredy cats of the team, love to watch horror movies.
And not just any horror movies; they're known to watch a marathon of Vincent Price's horror movies (More than 400 but less than 500 no less) whenever the one week marathon passes by.
Jaw Drop: Done in the series finale with Shaggy and Scooby once they see a commercial in the alternate timeline for Ricky Owens and Cassidy Williams company, with Professor Pericles as their non-evil sponsor.
Jetpack: Both of the Kung Fu wizards who turned Crystal Cove into a battle ground in episode 18 had jet-packs in their costumes enabling them to fly.
Karma Houdini: The Cicada Monster's main motivation was to get back at the company for putting LANDFILL WASTE in their snacks! And it seems like everyone is A-Ok with this!
Subverted. Several episodes later, it's revealed they often get sued for their products and most of Mystery Inc. consider them terrible.
Justified later when it is revealed they have Corporate Diplomacy (basically they are their own country) and therefore cannot be sued.
The Killer Was Left-Handed: In "Web of the Dreamweaver", Velma realises that the Dreamweaver holds his orb in his off-hand. In the original illustration, the Dreamweaver held the orb in his left hand. However, the Dreamweaver now attacking the town holds the orb in his right, meaning he is a leftie.
It's made even worse when he states that Mystery Inc. is dead; basically he's giving up everything he had right then to find his past. Can't really blame him since the past 17 years of his life have been a lie.
Also, part of why the Gang are so eager to head to Miskatonic University. After all, they don't quite know how to relate to happy, friendly decent people who aren't living in fear of losers in costumes messing with them. Solving mysteries is the only way they know how to live so they have to head where the rubber mask brigade is to feel normal.
Let's Just Be Friends: Episode 22 has Velma give Shaggy the 'I don't feel the same way about you I used to' speech at the end of the episode; it's an ache that even pizza can't cure. But then Shaggy says 'Well, let's see if it can!' and goes back to his chipper self.
And once Velma spilled the beans about Angel in episode 25, and Shaggy being sent to military school, who knows if they ARE going to still be friends?
In episode 48, Shaggy questions whether or not the gang are supposed to be friends after the revelations from the Sitting Room realm.
Episode 52 has the evil Annunaki telling the gang that he was responsible for forging their friendship. They tell him he's lying, and this is cemented when the Nibiru Entity that consumed Professor Pericles feels pain when it tries to attack Scooby and the gang.
Let's Split Up, Gang: Perhaps taken literally on episode 11. At the start, Daphne and Velma split up from the boys and Scooby. Their rejoining to the rest of the mystery is edgy at best. The end has them all going separate ways being watched by Mister E's assistant from episode 6.
Love at First Sight: The Orc asks this to Velma after she fixes one of their motorcycles. Velma, being the Deadpan Snarker that she is, blatantly tells him that she does not find him attractive.
Lovecraft Lite: The whole story arc, but special mention goes to the the evil entity. It's a Parrothulhu, as it looks like a cross between Professor Pericles, parrot and evilest character around, and a floating octopus.
Magic Plastic Surgery: In "The Man in the Mirror", Brad and Judy have plastic surgery to turn themselves into doubles of Fred and an older version of Daphne.
Magic Skirt: In episode 18. The White Wizard carries Mai Le off by her feet, rendering her upside down, but her skirt doesn't fall over. And again later after Mai Le gets hung upside down in the snare set on the Blake yacht (which was disguised as Mai Le's escape vessel).
Averted in the Man-Crab episode when Velma visibly tries to keep her skirt down after being flung into the air by the Crab.
May Contain Evil: In "When the Cicada Calls", Destructdo is making snack foods that contain toxic waste landfill.
Meaningful Name: Possibly Professor Pericles. The Greek general/politician he's named after was supposed to have a slightly deformed head. Professor Pericles has a greatly inflated head, and an evil scar.
Porto, the donkey as well. "Porto" in Spanish means "to carry", and that's what a donkey does, being a beast of burden and all.
Mega Corp.: Destroido, the company run by Mr. E, which seems to exist solely to ruin the environment and create dangerous products. Also, according to Sheriff Stone, it is its own sovereign country, thus preventing him from arresting anyone involved in it.
Metronomic Man Mashing: In Episode 14, Captain Caveman snaps Jabberjaw out of a panic attack by picking him up by the tail and smashing him back and forth between two banks of lockers.
Missing Mom: In Episode 23, Scooby accidentally knocks a photo off Fred's mantel; his admiring the pretty woman in photo was cut short when Shaggy told him that that's Fred's mom who left town when Fred was very young; Scooby apologizes for being out of line and Freddy waves it off with a sad smile and talking about how he one day hopes to tell her in person that she is pretty.
So pretty that she came out of a magazine! Fred's parents are Brad and Judy from the original Mystery Inc; the Mayor took their son away and 'promised' the parents he'd protect him!
Mix-and-Match Critters: The Horrible Herd (part-cow, part-bee, part-piranha). Plus many more among the mutated abominations in Destroido's lab; such as a cat with human hands and some weird parrot/cat-looking creatures.
My Friends... and Zoidberg: Daphne's father delivers one when he is hosting a dinner for a visiting Chinese delegate in "The Dragon's Secret":
Van Ghoul is the specter-besieged central figure of episode 19, "Nightfright."
Velma's parents run a supernatural tour of the city, which references many ghosts from the original series, such as The Miner 49'er. When Velma's forced to work as a tour guide, she takes great pleasure in explaining to the gaping tourists just how fake each and every one of them were.
Velma's mother is wearing an unused Alex Toth design for Velma's outfit in the original Scooby Doo cartoon.
A Don Knotts caricature can be seen amongst the tourists in episode 1, and he appears again at the beginning of episode 9. Knotts famously guest-starred on The New Scooby-Doo Movies.
Nugget Nose AKA The Galloping Ghost (a very obscure 1978 Hanna-Barbera feature from Yogi's Space Race, an equally obscure show) can be seen during the historical montage about Gatorburg.
Mama Cass Elliot, another The New Scooby-Doo Movies guest star, is one of the attendees at the auction for a painting. Amazing feat, as she has been dead since 1973.
In "Secret of the Ghost Rig", while in her bedroom knitting an ascot for Fred, Daphne hums the theme from The New Scooby Doo Movies.
Also in that episode was Harry the ventriloquist's dummy. Shaggy threw his voice a few times in the classic series.
In episode 8, Velma calls Daphne by her old nickname "Danger-prone Daphne" after she falls into the hidden door inside a tree.
Like the What's New episode "Large Dragon At Large", Velma bristles at the thought of wearing an Olde English maiden's outfit. Unlike the What's New episode, she doesn't wear one.
In a web game tie-in, one sidequest has Shaggy and Scooby collecting scattered pages of a play script. Shaggy notes that the play's set in a town called "Coolsville" (from A Pup Named Scooby-Doo and the live-action movies) and the main suspect is named Red Herring (also from Pup).
The Monster Museum in the beginning of Episode 20 sees a statue of Flim-Flam (who Daphne described as getting 25-to-life, despite being a pre-teen con artist), and when she sees a statue of Scrappy Doo:
Episode 21: Linda Cardellini, Velma from the live-action theatrical Scooby Doo movies, is the voice of Hot Dog Water. That makes two members of that cast giving voices to this animated edition.
The high-tech costume and superweaponry Alice May used in her Oblivia the Obliteratrix disguise were supplied to her by a man on Destroido's payroll: Benton Quest.
The pose for the yearbook photo of the original Mystery Inc is similar to a pose that Scooby's Mystery Inc had in Scooby Doo, Where Are You? theme song.
The current-day Mystery Inc also strikes that pose at one point.
Episode 27: Crybaby Clown tells the gang that Mano Tiki Tia (original series ep "A Tiki Scare Is No Fair") and the Ghost of Redbeard ("Go Away Ghost Ship and Ghostly Creep From The Deep") are nothing compared to him.
Episode 37: The seal named Scooby was seen eating a box of snacks with Scooby written on it. Also, he and his friends are from the Moby Dick segments of the Hanna-Barbera cartoon Moby Dick and Mighty Mightor, and their fathers are from the Hanna-Barbera cartoon Sealab 2020.
Episode 39: Charlie The Robot from the original Scooby-Doo, Where Are You! cartoon plays a key role in the mystery.
In "Heart of Evil" there is a Scooby Snacks box on the table. Also, when Scooby and Dynomutt meet, their high-five routine is exactly the same as Scooby and Scooby Dum in the opening sequence of The Scooby Doo Show (which was the other half of The Scooby-Doo/Dynomutt Hour).
The Final Episode where the gang decide to head out to the other side of the country via roadtrip and solve every mystery they come across along the way. Pretty much a reference to the original series.
The first three episodes of season 2 feature Daphne dating Baylor Hotner.
Nonuniform Uniform: In episode 9 Fred gets the gang team uniforms that make them look like a 70s Japanese supergroup. They're all similar white jumpsuits except that the color of the trim, piping, and ascot of each corresponds to a color of their previous outfits. It only lasts the one episode.
Daphne recalls how her dad was once found naked gnawing on a soup can when her mom was out of town.
In another episode Daphne talks about how every time her mother would sleep in their backyard treehouse, her family brings in a doctor or someone with authority to "work things out". Then they lock her away for a few months. In another, they have it to where Daphne mentions they used to have a lot of Faberge eggs, but she kept trying to boil them.
In episode 25, she mentions how one of her older sisters trained chickens to spell out her name as part of being engaged.
No Place for Me There: In the new reality created by defeating the Entity, Crystal Cove is built on beaches and sunshine, where people have a happy ending and all lost to the entity live again. However, such a place is without mysteries, and thus to satisfy their eternal craze for Mysteries, the gang leaves town for Myscatonic University and a whole host of mysteries that would follow along the way. It's a world they don't belong in anymore.
Not a Date: In episode 35 Sheriff Stone and Mayor Nettles insist that their obvious dates are stakeouts.
Not Wearing Tights: The villain in episode 17 has no secret identity. He doesn't reveal himself because he mistakes them for the first Mystery Inc, who already know him.
Official Couple: Velma and Shaggy are dating, but Shaggy does not want to be public about it. As of episode 10 the relationship seems to have been scuttled. Fred and Daphne date and as the show progresses they get engaged and, at the end of the first season, they split up as Fred goes to find his real parents.
As of the season 2 premiere, Fred and Daphne has sunk. Daphne has moved on in her life away from Fred and mysteries, and Fred just needs a big hug right now.
Perhaps not. Since then, Daphne has rejoined the gang after they rescued her from the Crybaby Clown, who turned out to be her new boyfriend, though she hasn't yet decided whether to take Fred back or not.
It looks as if Mayor Nettles and Sheriff Stone are becoming an item now. This exchange after they wrap up what caused the destruction of Cassidy's radio station:
Mayor Nettles: Van Ghoul, here we come!
Sheriff Stone: (casually) I'll get my smoker.
Oh Crap: In Episode 39, the old Mystery, Inc gets this when they finally get the disk pieces Freddy was hiding. The entire episode was a trap set by Freddy, whom they didn't think knew of their plans or was smart enough to trick them. He planted fake disks to be stolen while they stole Prof. Pericles' pieces, and they left a video disc in place of the pieces to explain everything.
In the Series Finale, the Nibiru Entity gets a satisfying one when he realizes the gang just launched an attack that's going to destroy the crystal sarcophagus, and him with it.
Out-Gambitted: The previous Mystery Inc. in 39 thought they'd gotten the Planispheric Disk pieces Mystery Inc. had, only to find out the pieces they'd stolen were fakes and Mystery Inc. was behind the Monster of the Week in their own successful plan to steal the pieces they had.
The gang's parents seem to put their happiness before their kids. Velma's mom (as shown in a picture) cares a lot more about her horses than her own daughter, Shaggy's parents think of him as an embarrassment, Fred's dad was thrilled at the idea of his son dying at the hands of the cicada monster, and Daphne's mother told her right to her face that sometimes she wishes they had a boy instead.
ALL the parents of Crystal Cove fit in this trope. When their children are "spookified", they abandon them!
Mayor Jones just has to be the worst out of them. For starters, he's not Fred's real dad. Though Fred's real father and mother end up topping him once they show up and get corrupted by the curse too.
The Picture Came With The Frame: It is revealed in Episode 26 that the picture of Fred's Missing Mom is a magazine photo. The Mayor isn't even his real father. His parents are Brad and Judy from the original Mystery Inc.
Prisons Are Gymnasiums: Grade-school-age Mary Anne Gleardan is incarcerated and learns to lift enormous barbells and and kill with her braids.
The Psycho Rangers: The original Mystery Incorporated are this in season two. The group falls apart quickly though, showing the consequences of distrust between friends, and teamwork being motivated by greed.
While Cassidy Williams is not Evil she does agree to work with the original Mystery Incorporated before betraying them, making her a token good teammate and counterpart to Velma. Velma struggles with feeling of love and betrayal for Shaggy, is distrusted by the current Mystery Incorporated for keeping secrets, and works for Mr. E behind her friendsí backs. Cassidy Williams struggles with feelings of love and betrayal for Ricky Owens, is distrusted by the original Mystery Incorporated for sharing secrets with the new Mystery Incorporated, and helps the current Mystery Incorporated survive the original Mystery Incorporatedís attacks.
Punctuated! For! Emphasis!: Used several times throughout the course of the series. One of the most notable examples might be Scooby-Doo at the end of Episode 51.
Scooby-Doo: Professor Pericles is going to regret the day he ever messed with Scooby. Dooby. Doo.
Real After All: Episode 41, the friar's ghost really was trying to warn them. And from the looks of things, the overall mystery of the disk, might actually be supernatural too.
Velma has a Heroic BSOD in episode 48 in regards to this as she's normally skeptical about the supernatural, and her trust of logic and facts in helping to solving the gang's cases had failed her.
You also see the ghost of the Captain of the Conquistadors in a previous episodes, who turns to bone and fades away laughing evilly.
Reality Ensues: Episode 33 when Sheriff. Stone tells Velma and Scooby about all the unlawful arrest charges against him from the gang's incorrect assumption of who was behind the monster of the week. When Stone finally thinks he's got a legit tag, the perp (Count Evallo) claims diplomatic immunity.
Reasonable Authority Figure: Mayor Nettles in season two who, unlike the previous mayor and most of the adults in general, is generally supportive of Mystery Inc.'s actions. In fact she actively worked to get the group back together in the season two premiere.
Redemption Equals Death: In Episode 17: Danny Darrow, the last survivor of the Darrow family, had booby-trapped his mansion in order to keep hold of a clue to the Haunted Treasure. Upon realizing that he'd wasted his life, he told the gang to take it and escape from the collapsing dwelling. His last words were "I hope it brings you more happiness than it ever did me."
Episode 37 starts with the gang still not trusting Angel/Cassidy. At the climax, after Professor Pericles sets off explosions destroying the underwater city, Cassidy stays behind to unhook the claw holding the Moby Dick submarine tail so the gang can escape. Everyone learns that Cassidy did not survive when Scooby (the seal) finds her diving helmet, shattered.
Episode 52 has Hot Dog Water holding Pericles in check so the gang can enter the gateway towards the cursed treasure, but she gets tripped up by Brad and Judy. Pericles' robots take aim at her, and moments later as the gang cross a bridge, the clatter of gunfire sounds in the distance. Scooby turns his head back and whimpers, and Velma sadly says, "Just keep going, Scooby."
Same episode: Mr. E/Ricky, who had already rebelled against Pericles, staves off one of the robots so the kids can destroy the entity but he is consumed by it seconds later.
Thankfully, thanks to the gang destroying Nibiru, the timeline was re-written and Cassidy, Ricky and Marcy are all now quite alive.
Relationship Reveal: The show decides to stop holding back, taking the long implied tease between Fred and Daphne and less-teased-but-not-entirely-fanon thing between Shaggy and Velma and canonizing them, in about as blatant a way as they could get away with.
Remember the New Guy: A character that was not seen until an episode acts like they have been well known. Though expect this character being the bad guy.
Ret Gone: After defeating the Nibiru entity, the timeline collapses to create one where he never existed, and any trace of his existence has vanished with him, such as his negative influence on the people of Crystal Cove's lives, creating a much Lighter and Softer world.
Retro Universe: Inspired by Scooby-Doo, Where Are You? and the 1960s, with 21st century tech and snark. Which some have decided to dub "Cyber-Funk".
The Reveal: in episode 46, we learn from a possessed Nova that Scooby-Doo, Professor Pericles, and other intelligent/talking animals like them are descendants of the animal hosts of Anunnaki, beings from another dimension with no physical form in ours, who come to Earth when Nibiru, revealed to be the time when the worlds are closest, occurs. While some have helped humanity through the ages, the one sealed in the crystal coffin is pure evil, and must not be released.
Rhymes on a Dime: The Phantom and the Freak of Crystal Cove. Dark Lilith, as well.