Daphne and her sisters: Daisy, Dawn, Dorothy, and Delilah.
Adrenaline Makeover: Principal Quinlen in "The Mystery Solvers Club State Finals". She starts off as very nervous and upset but the frantic pace and perils of the mystery causes her to lose her ponytail, glasses, and the top buttons of her blouse, and gains a more adventurous attitude.
Adult Fear: It turns out that Fred Jones Sr. kidnapped Fred as a child, taking him away from his real parents and feeding lie after lie to him, bringing the issue of parents not just lying to you, but not really owning you and treating you that way.
Adults Are Useless: In Episode 2 none of the parents can give the kids a ride home, for reasons such as "I just got comfortable" and "It's dark out there". The kids were stranded alone in a small suspicious town that had recently been having people disappear.
Not all adults are. Velma's mom knows a lot about the supernatural and the gang goes there when they don't have a lead on monsters. And in episode 25, Professor Hatecraft helps the kids even going as far as to stand up to the monster of the week.
In the season 2 premiere, the only slightly competent adult is the new mayor, who immediately agrees on the disguised Velma's advice to help get Mystery Inc back together to deal with a new threat to Crystal Cove. Every other adult is completely useless, holding out for a hero, and immediately willing to pay off the villain to go away.
By the second half of season 2 she is the competent adult.
Affectionate Parody: The second half of episode 10 is a shameless parody of the Terminator films. Several shots are almost identical to those used in the film, such as only half of the Fright Hound's face being pulled off or the fully robotic body rising out of the fire, without a scratch on it. Oh yeah, and there's also the mech from Aliens
"Escape from Mystery Manor" is a riff on the Saw movies.
Afterlife Antechamber: The place in Nightmare In Red is described as the boundary between life and the afterlife, and it holes the best aspects of the people living there El Aguirre feels that he and his men should remain there as they unleashed the monster. Cassidy Williams, Ed Machine and the previous (deceased) members of Mystery solvers clubs all are presumably stuck there.
The room also holds the better sides of still-living people corrupted, including a teenaged Ricky Owens, what we can assume are the parental and loving aspects of adult Brad and Judy, and the paternal side of Fred Jones Sr.
Episode 24: Fred finally gets the message. He proposes to Daphne.
Episode 26 gets Daphne to reveal they are engaged but when Fred finds out about his past, let's just say that these two won't be married for quite some time.
Episode 30: Daphne now simply wants to be friends with Fred.
Episode 31: Scooby falls for Brad and Judy's cocker spaniel Nova, and he asks the two people about love that he shouldn't: Fred and Velma.
All of the Other Reindeer: The locals treat the gang as, at best, a nuisance and, at worst, a group of destructive vigilantes owing to their inconvenient habit of saving a town filled with stupid, submissive and greedy jackasses from themselves.
As Velma states in the season 2 premiere, "The town hates us when we're not needed, cheers us when we are".
All Part of the Show: This is what happens when the ghost of Friar Serra attacks the production in "Theater of Doom". Director Vincent Van Ghoul gets hailed as a genius.
All Up To You: Scooby Doo and the other non-human sidekicks have to solve the mystery when the teenage sleuths are abducted in "The Mystery Solvers Club State Finals".
Taken literally in Episode 26. The gang has broken up due to Fred going to find who he is, Daphne chewing out Velma for her keeping Angel's identity all to herself and Shaggy being sent to military school. Scooby swears to Pericles that he's going to bring the gang back together to hunt him down.
Episode 27: It's Velma who has taken the initiative. Disguised as a mysterious stranger, she tells the new mayor of Crystal Cove, Janet Nettles, to get Mystery Inc. to solve the mystery of the Crybaby Clown. Scooby escapes from the farm and is rescued by Mayor Nettles, then he springs Shaggy from military school. The disguised Velma then rescues Fred from being blown up by the Crybaby Clown before revealing herself. Daphne has a new boyfriend and now she thinks mystery solving was all a waste of time.
Velma and Scooby tackle the mystery in episode 33 themselves when Fred, Shaggy and Daphne are otherwise preoccupied.
It's all up to Shaggy and Scooby to stop the evil ska band from episode 44 from causing all the citizens of Crystal Cove from dancing themselves to death.
In Episode 29, Shaggy, Scooby, and Fred are all preoccupied; Velma even comments that she and Marcie are the only ones who care about the case. Subverted when Fred ultimately solves it.
The end of the series implies that the original continuity may be the Alternate Timeline below.
Alternate Timeline: After destroying the evil Annunaki, the Gang end up in a Lighter and Softer world more akin to the original series. As an example of the changes, Crystal Cove is now billed as being the SUNNIEST place on Earth and all the tourism dollars are spent lauding the scenery.
Anachronism Stew: At the Ren Faire in episode 8, a number of people attend the medieval event as pirates. The staff are none too happy about this.
The show itself is stylistically set in what looks to be the 60s or 70s, vinyl records and the like have their place but such futuristic marvels like cassette players, compact discs and cellphones make appearances. Despite the presence of Laptops, desktops by in large are bulky and resember computers from the early 80's.
Ancient Astronauts: Revealed to be the primary forces at work in Crystal Cove in Season 2. Interdimensional beings known as the Annunaki utilize animals as vessels, causing them to talk and being responsible for a variety of mythological figures around the world from Egyptian and Sumerian gods to Sun Wukong and Quetzalcoatl, with talking animals such as Scooby Doo being explained as descendants of these vessels
Anyone Can Die: To show how really serious this show is. Season 2 really ramps this up as supporting characters start dropping like flies. The final has the Nibiru Entity eat the entirety of Crystal Cove. Its demise undoes it, but still!
Apocalypse How: Class 1.5, The series finale involves Prof. Pericles and the Evil Entity preparing to destroy the Earth by consuming all life on the planet, starting with Crystal Cove. Surprisingly evolves into a Class 6 example, but of course it's heavily inverted.
Arc Welding: Happens more and more frequently as the show goes on.
Arc Words: "This has all happened before" is the main one in Season 1.
Season 2 has "Nibiru..." and "The dog dies.."
Art Evolution: The characters designs are done in a much sharper, more stylistically simplistic way than ever before. Lampshaded in the second episode, when Daphne out of the blue asks Velma what happened to her hair.
Artifact of Doom: The Conquistadors' Treasure and the Planispheric Disk that leads to it are implied to be the reason Crystal Cove is cursed. There is some evidence that the curse may be real in "The Hodag of Horror" one piece manipulates its owner so it can be reunited with the others.
A Conquistador's spirit appears at the end of episode 34 once the gang takes off with the fifth piece. The spirit slowly disappears as it laughs, so yes, there could be a menacing curse.
And it's all coming together...the centerpiece of the Conquistadors' Treasure, on which Crystal Cove was founded upon, is a Sealed Evil in a Can, who has cursed the Disk to corrupt people and animals into seeking out all the pieces and finding the treasure, unleashing him from imprisonment, and causing doomsday to happen.
Scooby himself senses it in a nightmare in episode 46. He pleads to the gang to destroy the treasure once it's found.
As Long as It Sounds Foreign: The 'keys' to the Planispheric Disc the gang hunt down in the second season are marked in Spanish as "primero llave", "segundo llave", etc. Only problem is, llave is a feminine noun, so for the labels to be grammatically sound, they should say "primera llave", "segunda llave", etc.
Ascended Extra: Hot Dog Water appeared twice as a background/cutaway gag; eventually she's revealed as the villain in episode 21, and later as the replacement for Daphne in the Mystery Inc. Gang.
Gary and Ethan: Were just background characters, who gradually got more and more screen time, before being the villain(s) in Grim Judgement.
Ernesto and his activists appeared once as an activist group when the gang visit a college, and a few episodes later they reappear protesting Destroido, and they are the villainous fishmen in that episode.
Vincent Van Ghoul appears in a Mythology Gag movie series commonly seen on the television, before later appearing in person.
George Avocados first appears as the mayors rival, then as a guest at a dinner party, he becomes more important when its revealed that he's considerably poorer (Scarebear), and farms avocados, which are accidentally blown up he is the ghost in Theater of Doom, and upon his capture Fred exclaims "Yes finally! I knew you'd be the villain eventually," and he states that it was finally him after previous misdirects.
Back from the Dead: Everybody in the series finale that had just been killed by the evil entity. Once the timeline is reset, they all come back to life, including people like Cassidy Williams, who died many episodes prior. Basically all the deaths that were caused by the influence of the evil entity were undone.
Balloon Belly: Happens to Scooby and Shaggy in "The Devouring" when they attempt to devour all of the baked goods in Crystal Cove.
Bar Brawl: Episode 15: "The Wild Brood" starts off with a bar brawl between biker-punks and the orc-like Wild Brood. Asses get kicked.
Beard of Sorrow: After the events of the Downer Ending and his continued failure to find his parents, Fred begins season two sporting his "hobo look".
Big "NO!": Fred has one after it is revealed that the rest of the team won't go to the Mystery Solving contest due to Scooby being sick.
Big Screwed-Up Family: Daphne alludes to the Blakes being this, what with family meetings with shrinks and her mom being temporarily committed.
Fred's family is incredibly screwed up. His adopted father turned out to be a villain, who was only keeping him around as leverage to keep his actual parents at bay. However, his actual parents aren't much better as they made no attempt to contact him during their exile and, it's strongly implied they are just using him to get to the treasure.
Bittersweet Ending: The Nibiru Entity is destroyed saving the universe from doom! However it's a recreated/divergent timeline based on what happened without the Entity below Crystal Cove to corrupt it causing what should be idyllic lives for the gang... however they now feel like strangers in their own homes as these aren't quite the people or home they know. Worse yet, for them, this perfect setting seems to have no mysteries. A message from Harlan Ellison, who knows about the reality change, telling them to come to Miskatonic University perks them up and they resolve to travel across the country and while it means leaving everything behind they're now able to travel the road together doing what they love.
In addition to their own problems with the new world. Not everyone is better off. Daphne's sisters for example, who went from all being prodigies with high profile careers, to underachieving slackers with Daphne being the only one their parents can be proud of.
It's also implied that the series is a prequel to the existing Scooby-Doo universe, so all the Character Development over the two seasons will eventually be reset
Bizarro World: Crystal Cove, though it is revealed that all the madness in the town is caused by the effect of the evil entity being buried directly underneath it.
The gang also feels this way about Crystal Cove, the SUNNIEST place on Earth. All the people and things that they've become used to are now reset to be better, but this makes the gang feel like they don't know anything and don't belong.
Blind Without 'Em: Velma in episode 32. She even lampshades it after Randy Warsaw removes her glasses with the idea of her being an art inspiration and she looks at herself in a mirror.
Breather Episode: Episode 40, with Blue Falcon and Dynomutt. Mind you, Blue Falcon is a walking homage to Batman as written by Frank Miller, but the whole thing is basically played for laughs and but for a sole scene has no immediate effect on the rest of the series.
Broad Strokes: Contains many echoes of the original series in a modern setting.
Brown Bag Mask: Sheriff Stone dons one to conceal his identity after he loses his job in "Dead Justice".
Call Back: This may or may not be intentional, but in episode 41, "Theater of the Doomed," the ghost of the friar warns them to heed the alligator's warning, and says "The dog dies" before vanishing. In episode 2, "The Creeping Creatures," the episode with the alligator monsters, the gang visits The Drowsy Gator. Pool, Food and Sundries. Certain letters in the neon sign die out to spell "The dog dies."
Cerebus Retcon: Freddy's motive for his trap addiction; Mayor Jones lied to him saying that his mother left them and Fred thinks that traps keep people from running away. Essentially Mayor Jones' humorous neglect gets this when its revealed that he is basically keeping Fred his hostage.
Cerebus Syndrome: The show has always been somewhat darker than other Scooby-Doo incarnations, but became especially dramatic and creepy from the season 1 finale onward.
Cell Phones Are Useless: Subverted. The gang has cell phones that work when they are stranded in Gatorsburg, but they reach indifferent parents who are unwilling to help, so it's really Adults Are Useless.
Chainmail Bikini: In "Pawn of Shadows", the Obliteratix's battle costume consists of a mask and strategically placed leather straps.
A subtle example would be Velma's parents. In the first few episodes, they appeared to be just as thoughtless as the other parents, but as the show progressed the gang would go to Velma's mom for advice on the supernatural. She even helps them during a case involving a headless zombie, and once offered to "take care" of Shaggy with a poison mushroom beverage after he chose Scooby over Velma (she said she was kidding). Granted, Velma's mom still got in a couple of snarky comments here and there, but her reveal that she actually reads Velma's blog is something you'd expect of a typical parent. And, by the disastrous events of the last episode, the Dinkleys are the only parents shown comforting their child and not making the situation worse.
Chekhov's Gunman: Many of the Ascended Extras are at first unimportant, then vital, or at least important to the episode, like George Avocados, Marcie Fleach, or Gary and Ethan. Harlan Ellison is just a book-writer whom Angie knows, and is friendly to H.P. Hatecraft at the very end, he reveals he knows about parallel universes, and knows what the Cosmic Retcon was.
About half the time, the gang's leads are off and they learn who the monster is at the same time the audience does. Jason even calls them out on jumping to conclusions when they accuse him in Episode 10.
Episode 2. There are only 3 people in this ghost town. There are 3 alligator people scaring visitors away. Who could the alligator people possibly be?
Everyone except Velma in episode 33. She's the only one who suspects the cemetery groundskeeper to be the Graveyard Ghoul, which it turns out to be, and nobody else believed her. (Scooby followed Velma because he trusts her instincts and he was worried about her.)
Code Name: Episode 31 has the gang communicating via walkie-talkie with the code names "Smart Girl" (Velma), "Smokin' Hottie" (Daphne) and "Scarf Boy" (Fred).
Cold Open: Up to episode 47, every episode had a cold open. Up to episode 46, all season two episodes had a "previously on" recap.
Comedic Sociopathy: After causing a patient to flat-line due to a panic attack, all the gang merely walks out with Freddy commenting that the questioning had gone well.
Comically Missing the Point: Daphne's mother mentions that she's been taking night classes to become a notary, and states that knowledge is more important than beauty. Then she says that she's going to find out what a "notary" actually is before the final.
Compliment Backfire: "Oh Velma, you're very pleasant when you aren't trying to be smarter than everyone else."
Conspicuous CG: Most non-human motion tends to do this, especially moving cars.
Consulting a Convicted Killer: In "Wrath of the Krampus", Mystery, Inc. visit the prison to consult with the grade-school-age Mary Anne Gleardan, one of their former antagonists.
Velma's family owns a museum filled with "monsters" that have haunted Crystal Cove, many of which the gang has debunked.
In fact, in the pilot she's guiding a tour through the museum, and is reprimanded by her parents for ruining the tour by revealing who was under the masks when they were finally caught.
Episode 6 can be considered a huge one of these, considering the villain is Alice May, who poses as Alice Carlswell, daughter of the gang's iconic villain "The Creeper".
An in-series nod in Episode 10. The Mystery Machine runs out of gas and slows down, and Daphne says "Don't tell me the engine is missing again!" referring to when Mr. E removed it in episode 2.
Another in-series nod in Episode 15. After the cold open, the episode starts off at the Tiki nightclub, where Sheriff Stone congratulates Mayor Jones for re-opening the club after it was destroyed by the Humongonauts from Episode 9.
Yet another in-series nod in Episode 20; simply put, Scooby still has no idea what, if anything, Skipper Shelton is talking about.
More in-series references: The two teens who got abducted from Episode 4's Man-Crab reappear as victims of the Manticore. As well as the owner of the amusement park wondering how they're going to sell their stock of Que Horrifico shirts and Char Gar Gothikon plushies.
Episode 24 has Daphne worry whether her seafood allergy from Episode 4 will act up with all the oysters around.
Episode 25 not only has Hatecraft show up again, Alice May is back messing with the gang in a different costume.
Episode 38 has the gang visiting the local jail. Watch the background; every inmate is one of the previous villains.
Episode 48: All the people associated with the treasure appear in the dream sequence: "Benevelent Lodge of Mystery, The Darrow family, the original mystery inc, even Ed Machine and Fred Jones Senior.
Cool Big Sis: Delilah Blake, one of Daphne's sisters, is in the military, speaks like a drill sergeant, and is just about the only member of Daphne's family who has made an effort to comfort her and offer her help, even telling her to call if she needs her.
Cool Car: The Mystery Machine, especially with the improbable moves it pulled out against the ghost truck, as well as the impossible jump-flips it did while trying to shake off the Fright Hound.
And that's not to mention the Enigma Engine from the previous Mystery Inc. Gang.
Cosmic Retcon: The demise of the Nibiru Entity erases it from existence. As a result, its influence is removed from history, changing Crystal Cover to a normal, happy town and giving the original Mystery Inc the lives they should have had without his influence.
Continuity Reboot: The whole series. Done in-universe in the series finale, where the destruction of the Nibiru Entity causes a reset in the time stream, and the gang is placed in an alternate universe where the evil of the treasure of Crystal Cove never negatively influenced anyone's lives.
Crazy-Prepared: In Episode 21, Fred explains to Velma that he gave the Planespheric disc piece to Shaggy and Scooby cause they'd be the last person to have it. Episode 26 reveals that Shaggy and Scooby do have it in a bed/fridge that they keep in the case that they don't get an evening snack before bed.
Episode 25 reveals that Quest Laboratories is a subsidiary of Destroido. And episode 38 shows that Destroido is owned by Ricky Owens/Mr. E.
Season 2 is set to feature more of the Quest family, along with Dynomutt and Blue Falcon (those two will appear in episode 40).
Episode 37 features Tom and Tubb from the old Moby-Dick cartoons, along with their pet seal, also named Scooby (Moby has been reimagined as a whale-shaped sub). And their fathers are referred to as being Paul Williams and Michael Murphy.
In a recent commercial at AMC Theaters, the Gang find the one guy who didn't turn off his cell phone: Daffy Duck.
Cut Lex Luthor a Check: Almost every single villain is shown using fantastic inventions, sometimes explicitly called military tech.
Played straight by the handful who are using said inventions to directly steal money or protect their illegal money-gathering schemes.
Averted in other cases, where the villains were settling personal scores or pursuing social goals.
Justified in that apparently all of the villains were being manipulated by the Nibiru Entity's presence.
In a non-villainous example, the townspeople — particularly the sheriff and Mayor Jones — are angry that the gang debunks the various hoaxes, consequently ruining potential tourist attractions. Except that, because of their grandiosity and complexity, the hoaxes themselves as hoaxes would make a good tourist attraction.