In the penultimate episode, Marcie gets shot to death offscreen. She comes back the next episode along with all the other dead characters when the Evil Entity is destroyed, but still.
Dartboard of Hate: In the episode "In Fear of the Phantom", when it is explained that Daniel Prezette was disrupting the Hex Girls' concert as the Phantom because he hated the Hex Girls for ruining his musical career, a flashback shows him throwing a screwdriver at a picture of the Hex Girls.
Demonic Possession: played with, episode 46 reveals that talking animals like Scooby and Pericles are descendants of animals once possessed by Annanuki during the periods that their reality is closest to the earthly one, and the Annanuki possessing Nova reveals that while some are benevolent, the one within the crystal coffin with the treasure is EVIL, and must be destroyed.
Despite the Plan: Averted every few episodes where Fred's traps actually work. Lampshaded in episode 9.
Velma's Mother: "Good thing I have this spare key so I can search your room when you're not home. (Beat) Oops, did I just say that out loud?"
Did You Just Punch Out Cthulhu?: In the season 2 finale sees the gang kill the Nibiru Entity by severing the connection it was using to draw power from another dimension, resulting in the connection imploding and erasing it from existence.
In "Where Walks Aphrodite", Angel Dynamite is immune to Aphrodite's pheremone attack because she suffers from anosmia (i.e. she has no sense of smell).
In "Dance Of The Undead", Rude Boy and the Ska-Tastics' music is not sending Shaggy and Scooby into hypnotic dances like everyone else because Shaggy is tone deaf and Scooby says that music is just noise to dogs.
Disproportionate Retribution: In "Dreamweaver", the criminal of the week attempts to ruin his former friend's lives because his in-game character died when they played an RPG together back when they were kids.
Does Not Like Men: Marcie (aka Hot Dog Water) seems to take it as a sign of weakness to need help from a man.
Fred's magazine "Traps Illustrated" has a woman in a bikini on the cover. His reaction to Daphne finding it is similar to someone hiding porn. It's a reference to Sports Illustrated with its famous swimsuit issues, though Fred's "I read it for the articles" invokes Playboy.
"Grim Judgement" has two teen boys stalking and assaulting women they want as girlfriends.
In episode 7, the Hex Girl's manager used to be the manager of a singer called Fancy Pants. After he was dropped by his old label, the manager mentions that Pants "went down the rabbit hole." Consider for a moment what that's slang for, and what some rock stars get involved with when their career hits a rocky patch...
In episode 8 Shaggy and Scooby watching the Renaissance Fair announcer who says he hates pirates secretly dresses up like one. It's made to seem like watching him dress up in women's clothing. Even Scooby says his "brain needs a shower."
For a non-sexual one let's go back to episode 21 with Angel and Velma. Angel tells Velma to keep the identity of her as Cassidy Williams a secret. Now compare that to the first 10 episodes with Velma's relationship with Shaggy. We all know that keeping secrets never leads to anything good. Specifically because the gang is broken up and Daphne has blamed Velma for causing this for keeping Angel's identity a secret.
Another nonsexual one: Velma suspects a gravedigger for the monster of the week based solely on the way he looks and his odd grumpiness. Fred dismisses this as "villain profiling."
Doing It for the Art: Used in-universe. The reason Baylor Hotner initially became Crybaby Clown, to do research for his next film.
Downer Ending: For a season finale no less! The Mayor was the freak who caused all of the mess in the first place, Pericles has 2 of the 6 Planespheric Map pieces, the gang is broken up, and Fred is off on his own to find his real parents. Here's hoping to Scooby fulfilling his promise to get the gang back....
And the second season premiere, if you can believe it, ends on another, nearly as grim a downer ending where The Bad Guy Wins, Fred's confidence is destroyed and Daphne refuses to come back to mystery solving.
Episode 37. Cassidy, from all indications, did not survive the detonation of the undersea city while trying to free the submarine's tail. Plus, Professor Pericles has made off with the sixth piece of the Planispheric Disc, giving him three pieces and the gang three pieces. Tony Cervone confirms on Twitter that Cassidy did not survive.
Episode 42: Just as the gang finally has a lead on the treasure as told by the Planespheric Disc, they return to see the City Hall/their base of operations up in flames, caused by Brad and Judy.
Episode 43: The town is in ruins, the gang have inadvertently released a ravenous and aggressive species into the ocean ecosystem, and Nova's barely clinging to life.
Dream Within a Dream: Scooby experiences one at the start of "Stand and Deliver." He dreams he is sharing a romantic dinner with Nova when it is attacked by killer robots. He then wakes up in Nova's hospital room, which is then attacked by the same killer robots. He then wakes up for real and blames the dream on eating too many doughnuts before going to sleep.
You'd think that after being saved from an Eldritch Abomination, even a faux Eldritch Abomination, would make the rescued party grateful enough to spare you a lecture on proper grammar.
The Motive Rant for "Lord Infernicus" in "Mystery Solver State Finals."
Early-Bird Cameo: Skipper appears in episode 3. In the next episode, he's a prime suspect.
Mr. Chen, as well as his cafe, are introduced in episode 15. They are featured in a more prominent role three episodes later.
Hot Dog Water made a brief appearance in episode 16 when Velma recognizes her in class affected by Aphrodite. She then makes another cameo in episode 18. Episode 21 had her be an employee and attacker of the amusement park that the manticore attacks. She then went on to get a major role in the second season.
There is also Ernesto and his group of environmentalists. They first appear in episode 12. They appear again in episode 20 as the Fish Freaks.
The Quest Team, who were first seen in the Obliteratrix's confession flashback appear again in a season 2 episode as part of the Blue Falcon's origin story.
An early episode has Ed Machine mistakenly voiced by Lewis Black, giving the impression that Machine is actually Mr. E.
The first episode features the trap Fred built failing due to him and the members of Mystery Inc being in completely the wrong place, like how the traps never worked in the original series. Fred's traps have a greater success ratio in almost every other episode of this series. Something similar will happen several episodes later, when the gang is surprised when Fred's trap works. While this Fred doesn't have a 100% success rate, he certainly wins more than he loses so the comment makes no sense.
Earn Your Happy Ending: EVERYONE. When the Nibiru entity is destroyed, it retroactively erases its influence from time. Fred's parents are not psychotic and are dual obstetricians, Daphne's parents are highly supportive of her and her plans to marry Fred, Velma is best friends with Marcie, Shaggy's an award winning chef, Fred Jones Sr. is the upstanding principal of Crystal Cove High and considers Fred to be like the son he never had, Sheriff Stone and Mayor Nettles are married and have four kids, and Ricky Owens runs an environmentally friendly corporation alongside his wife Cassidy, with Professor Pericles as their sponsor, and Danny Darrow is the dean of Darrow College, and has turned his family's old mansion into a historical site. No one has been corrupted or gone crazy and Crystal Cove is not a haven for masked psychos. At first this seems subverted for the Gang as they're left with no place in Crystal Cove, as mystery solvers have no place...then they get a call and realize the world has mysteries aplenty, paint up Fred's van as the Mystery Machine and head out to solve them.
Subverted by Daphne's sisters though, who are revealed to NOT be successful in their respective careers, though they were kinda jerkish anyways
Earthquakes Cause Fissures: The cold open in Episode 17 starts off with this during a flashback, swallowing a mansion up underneath it. An earthquake appeared at the end of the episode, but it's not stated what happens after that.
Char Gar Gothicon, monster of "The Shrieking Madness."
The Nibiru Entity. And unlike Char Gar Gothicon, it's real.
Eldritch Location: The Nibiru Entity's lair has a bunch of areas requiring the use of "keys" (an old Flintlock pistol, a Conquistador helmet, a bowl, and a piece of cloth). The first one in particular is an area that seems to take place in a sky-like area.
In "Nightfright", Vincent Van Ghoul starts the laughter at the end of the episode with an Evil Laugh and everyone else joins in.
Scooby, the gang, Blue Falcon and Dynomutt at the end of episode 40.
The series only has one laugh track ever played, which is in the series finale after Scooby-Doo says his catchphrase, wrapping everything up on a positive note. Worth noting that this also takes place in the altered timeline — the original timeline never had one.
Everyone Calls Him "Barkeep": One of the background characters is a classmate known as "That weird girl, Hot Dog Water." In an episode 18 flashback, she says she's gluten intolerant.
Hot Dog Water returns in season 2, filling in for Daphne's spot for the first three episodes. She remains an ally of the gang.
She reveals her real name in episode 28. It's Marcie Fleach.
And to Velma, since he was The Smart Guy in addition to the Team Pet. The other former members of Mystery Inc (except for Angel) have also developed into this, with Mr. E being the Evil Counterpart to Shaggy, and Brad Chiles and Judy Reeves to Fred and Daphne.
Evil Is Not a Toy: Pericles ultimately ends up releasing the Nibiru Entity, and sacrifices his body to it, thinking that it might give him some kind of supreme power. It kills him, and devours the other members of the old Mystery Incorporated as well.
Evil Twin: The Fright Hound in episode 10, to Scooby.
Design-wise, Alice May is a blatant one for Gwen Stacy: same hairstyle, hairband, and green-striped clothes.
Gus, or "G-man" from episode 7 is basically the eccentric Ronnie "Z-man" Barzell from a certain creepy schlock film. In addition to looking exactly like Z-man, he talks with his faux-British accent and mannerisms, as well as being a record producer with a taste for alt bands.
Jason Wyatt from episode 10. What with being a nerd, having great scientific know-how, and adores/admires Velma... It's "What's New Scooby Doo?"'s new form of Velma-stalker Gibby Norton!
Ernesto from Episode 20 is a die-hard environmental protestor. He is also Che Guevara, even down to his first name.
Episode 40: Blue Falcon is turned into a Captain Ersatz of Frank Miller's Batman. Velma even lampshades the dubious need of a vigilante.
Scooby Snacks looks like a different color scheme for a box of Cheez-Its.
Pretty clear Chargargothica, the monster with no name is an Expy of Cthulu, given that Cthulu runs similar circles in having a "hard to pronounce" name with the human tongue, and having tentacles. He physically looks a little like Davy Jones, too. Also, makes sense as Hatecraft is a pretty blatant expy of Lovecraft.
Mr. E in the alternate timeline is pretty clearly supposed to be Steve Jobs.
FaceHeel Turn: Former members of mystery solving teams have a habit of becoming enemies to the next generation.
Fan Disservice: Episode 24, when Night Ranger takes his shirt off to use a bale of hay for a punching bag (It Makes Sense in Context). Daphne pretty much speaks for the viewers when she asks "why did he have to take his shirt off?"
Fanservice: Daphne has a strange habit of walking around in her underwear and wearing bikinis and other Stripperiffic outfits on a regular basis.
Fantastic Racism: Hilariously played with the Wild Brood. Everyone treats them suspiciously, but this is due to the fact that they are a motorcycle gang and not because they are Orcs. However, when they take off their masks to reveal that they are video game developers and geeks, Sheriff Stone suffers a full-on panic attack and asks them to put their masks back on.
Foreshadowing: A fair amount, much of it related to hinting at the mysterious history of Crystal Cove and the identity of Mr. E.
First, we have the locket from episode 1. Members of the original Mystery Inc. had them and it was considered their symbol. It was Judy's locket and the picture inside are actually Fred's real Parents, which explains Mayor Jones' expression when he saw it!
Also take a good note at what Velma states about Crystal Cove's early history: it was found by Spanish Conquistadors. Guess what's important about them about 24 episodes later!
Then there's the newspaper clipping in episode 4. Part of it was cut off and Angel seems as if she knows something. She does, because the part cut off showed her when she was still known as Cassidy Williams.
Episode 6 shows someone getting Alice May to escape from jail. Said man is actually Ed Machine, the head of Destroido, who has relationships to Mr. E
Episode 10 has Professor Pericles spouting out that the gang has to keep an eye on those close to them; especially Fred. In episode 21, the Mayor is looking for something and Mr. E comments that Fred is getting in the way of saving the remaining members of Mystery Inc. Plus in episode 23, Pericles states that the Mayor stole something important from him, but said Mayor is in denial.
Mayor has a good reason; he made a deal with Pericles who would betray his gang. Then he betrayed Pericles and stole the disk piece. Then Pericles stole it back at the 26th episode and now Mayor Jones is going to be arrested.
Episode 12 has the Darrow Family Trunk filled with secret documents. Episode 17 lead them to meet up with Danny Darrow and episode 25 finally told them what they were looking for.
HP Hatecraft also claims that Char Gar Gothikon comes to him in his dreams to inspire his stories. While he admits that he lied in order to get the book to sell, the idea of an eldritch horror influencing people within their dreams matches the modus operandi of the Nibiru Entity.
Episode 16 has Pericles and Scooby teaming up and gathering items for an antidote. One of the places was at the old Spanish Church which holds the entrance to where the Haunted Treasure resides!
Here's another one: "I guess we're not a team anymore." Velma, you don't know what you caused.
A minor one. In the cold opening flashback of episode 17, Danny Darrow as a little boy is wearing a white beard as his Halloween costume.
Speaking of Danny Darrow, he nicknames Fred as Big Chin Man because he's really seeing Fred as the original Mystery Inc; member Brad Chiles, who happens to be Fred's father!
In episode 2 the lights that light up the letters of the The Drowsy Gator's sign flicker in such a way to read "The dog dies!", a simple little scene to scare Scooby. In episode 41 the mummy of Friar Serra, a member of a previous Mystery Inc. group hailed for saving Crytal Cove from an earthquake along with the group's donkey Porto, tells the group the real story. That Porto in fact had been corrupted by a piece of the Planispheric Disk and destroyed Crystal Cove. In every group the animal member has been the one to be corrupted and betray everyone leading Friar Serra to declare "Heed the warning of the alligators! The dog dies!" while pointing at Scooby.
Frank Welker voices the Freak of Crystal Cove, the Monster turns out to be Fred Jones Senior.
Fred and his dad look nothing alike. This hints at the fact that Mayor Jones is not Fred's real father.
For Want of a Nail: The tension between Angel and the gang probably could've been avoided if either Angel or Velma explained about Angel's real identity sooner.
The Cynic: Sheriff Stone, Major Jones and (to a lesser degree) Angel Dynamite.
The Optimist: Fred.
The Realist: Velma.
The Apathetic: Daphne.
The Conflicted: Shaggy.
Interesting to note is that while they fit this pattern philosophically and functionally Velma, Daphne and Fred have personalities more closely associated with Cynic, Optimist and Apathetic respectively.
Four-Temperament Ensemble: The gang appropriately match their own color schemes. Velma (Yellow Sweater) is choleric, exhibiting leadership when solving the mystery, but rather pushy, and a rather violent Tsundere at her worst. Daphne (Red Hair) is sanguine, the most cheerful and optimistic of the group. Scooby (Blue collar) fits into leuquine, as he is rather non-confrontational. Shaggy (Green Shirt) is phlegmatic, the Non Action Guy who runs away from anything spooky, and is only there to react to the situations. Fred is melancholic as he is obessessive (when it comes to traps) and emotionally high strung (when Daphne is in danger). He wears... white, rather than black, kinda crashing that color coded bit.
Velma vs Scooby over Shaggy. At first it seemed that Shaggy was using Scooby as a scapegoat to hide his fears of commitment, but it turned out his fear of telling Scooby was pretty well founded.
Also, Fred and Daphne.
Fred: Oh what the heck, going to the prom with a friend will be more fun than with a date anyway. Right? Daphne: *sigh* I'll take what I can get.
The Fred and Daphne thing has been averted as of episode 24. Fred has proposed to Daphne and the two plan to marry once they get to college.
Not anymore! Thanks to Mayor Jones' actions, he took Fred away from his real parents and now Fred is a) going to go search for them, b) broke up the engagement and c) broke up Mystery Inc.
Shaggy and Velma. Shaggy dumped Velma in favor of Scooby, then had a change of heart and wanted to try the romance thing with Velma again. She responded at first, but decided they should stay "just friends"... later revealing that she is still hurting over being dumped for Scooby, and apparently afraid if she took Shaggy back he'd do it to her again.
And turnabout occurs when Scooby abandons food and Shaggy for following his puppy love, Nova.
Funny Background Event: Scooby is harassed by an angry squirrel in the first episode, while the rest of the gang are talking to Prof. Raffalow.
"Scarebear" has Scooby and Shaggy be chased by a mutant owl while Daphne and Fred hit on each other.
Gainax Ending: The gang manage to defeat the monster under Crystal Cove, but in doing so erase it from existence and wind up in alternate timeline (implied to be the original series timeline) where everything is different and the treasure of Crystal Cove (and the monster within) never existed. However without it, there's no mysteries to solve and the town was never corrupted because of it. However, the group get a message from Harlan Ellison—who also has Ripple Effect-Proof Memory—and offers them enrollment at Miskatonic University where he works. The gang, giddy for a new adventure, accept and set off on a roadtrip towards there, vowing to solve any mysteries they come across along the way.
Generation Xerox: Their have been many versions of Mystery Inc., each having four people and a mascot, each having some variation on the name Mystery incorporated. In some case there is even a close resemblance between the group members.
More directly the Fred inherited his parents' trap obsession; and Angel when she was younger, was nerdy, wore glasses and was in love with owner of the mascot, Ricky Owens, which obviously mirrors Velma.
Gotta Catch 'Em All: The six pieces of the Planespheric Disk. As of the season 1 finale, Pericles has nabbed off with two of them. The other four pieces should be snapped up in season two as producer Mitch Watson has noted on his Facebook page that the series will only go 52 episodes.
As of episode 31, Scooby and the gang have pieces three and four. Professor Pericles calls a powwow in regards to this.
Episode 34 has the gang possessing piece no. 5 now.
Episode 37 has Professor Pericles with piece no. 6.
In episode 39, the good guys now have all six pieces, having retrieved the other three from Mr. E's lair thanks to a "Scooby-Doo" Hoax the gang themselves set up. But now Pericles has it in episode 47 (Fred gave it to him in exchange for Daphne, who was held captive by Pericles' robot goons) and he's summoning what he terms as his "master" with it.
Grand Finale: The series finale, where the Nibiru entity is defeated, and Mystery Incorporated also manages to (inadvertently) create an alternate timeline where the entity's evil never negatively influenced anyone's lives.
"Can anybody tell me what photosynthesis is? ... And PLEASE don't say plant farts."
Subverted in episode 36. In the Burlington mansion, the gang wants to get some sleep but Velma wants to check out the library. "Who can sleep with all those books?" She asks. The others raise their hands.
Hannibal Lecture: The gang gets one in "Howl of the Fright Hound", from a prisoner in the city's Animal Asylum: Professor Pericles, the mascot-pet—of the original Mystery Inc!
Hellish Copter: Seen in "The Horrible Herd" when the gang and Mayor Nettles ride in a helicopter; the herd of mutant bee-cattle cause some damage to it while in flight, then once among a safe landing and after everyone abandons it, the helicopter blows up, just like many things in the show do.
Heroic BSoD: This happens to Fred after Daphne is kidnapped by the crab monster and when a teacher has supposedly died (see Faux Death). Fred gets a serious case of this in Chapter 26.
Scooby and Fred are paralyzed in disbelief when they see Shaggy and Daphne kissing in episode 36 (they were both under a dream hypnosis). Velma snaps Scooby and Fred out of it by telling them they were only dreaming.
Velma gets one in episode 48. She feels that how the events that happen during the gang's hypnosis are devoid of any logic and thus her trust of logic and facts have failed her, so she breaks down and cries.
Episode 37: Cassidy stays behind to free the gang as Pericles detonates the underwater city. Cassidy does not survive.
Episode 51— Marcie, giving Scooby and the gang time to get away. We don't see what happens, but it's quite obvious.
Hero of Another Story: Before the Mystery Inc the show focuses on, there were several previous groups of four with one animal that solved mysteries together. Nibiru's influence led to most of them being driven to evil, always starting with the Team Pet.
Heterosexual Life-Partners: Shaggy and Scooby, played mostly straight but also hilariously subverted. On chapter 9, with the Friend Versus Lover between Scooby and Velma, Scooby used phrases like "You are cheating on me!" or "I gave him the best years of my life".
Hide Your Lesbians: Velma's relationship with Marcie (and earlier, Amy) seem like queer relationships that are stuck as subtext, especially by the ending of the series.
Velma is happy to have Amy as her "special friend", gets angry about the gang trying to "steal her", and is devastated to eventually find out that Amy is married.
In the finale, Marcie is casually hanging out in a bedroom with Velma and refers to her as "my girl." If this is meant to be relationship subtext, it wraps up loose threads about Velma's old attachment to Shaggy, which otherwise never gets resolved.
Episode 11 has Velma say "I guess we're not a team any more."
In Episode 26 Fred and Daphne develop a resentment toward Velma for keeping Cassidy's/Angel's secret. Fred also breaks off his engagement with Daphne to look for his real parents, Shaggy's parents plan to send him off to military school and Scooby to a farm, and the girls are grounded.
Humans Are Bastards: Many of the side characters are much more cruel, selfish, and greedy here than the other Scooby Doo incarnations have been. While the Mystery Inc gang are still the same nice and likable group of detectives that they have always been, almost all of them have developed an Adaptational Jerkass characteristic.
Daphne occasionally being more self-invested in the attention she gets from Fred.
Velma is more self-centered, sassy, vain, and sexually aggressive than she was in past incarnations.
Even Scooby is more stubborn in this one than he usually is.
Hyperspace Arsenal: Episode 25 has Shaggy lampshading the fact that Obliteratrix's costume has no pockets so where are all her weapons coming from?