Actor Allusion: In "A Scooby-Doo Valentine", Daphne laments that the fact that she was impersonated by an extra (who, ironically, resembled her voice actor, Grey DeLisle), saying "What, Sarah Michelle Gellar wasn't available?" Sarah Michelle Gellar played Daphne in the Live-Action Adaptation of the franchise.
Art Shift: In contrast to the usual Hanna-Barbera style, the characters are redesigned in Warner Bros. Animation's typical "house" style of the time for this series.
Berserk Button: In one episode, Freddy tells Shaggy and Scooby that the Monster of the Week was badmouthing Scooby Snacks; this gets them riled up enough to be bait without the usual bribe.
Big Eater: As always, Shaggy and Scooby are made of this trope.
Blonde, Brunette, Redhead: Occurs in the Halloween episode with redhead Daphne, brunet Velma and Velma's blond cousin, Marcy.
Continuity Nod: The flashback to the gang's childhood in "A Terrifying Round with a Menacing Metallic Clown" is in the same style as A Pup Named Scooby-Doo.
This series was actually full of nods, a first for a Scooby Doo series. The gang would reference places they had been previously as well as feature recurring characters in a few episodes. Even the Hex Girls made an appearance.
Covered in Mud: In the episode "Reef Grief!" Spencer Johnson covers the sand castle competitors with mud so they can build his underground freeway.
Crazy-Prepared: The show turns Fred into this, having modified the Mystery Machine to be able to turn into a submarine. In "Wrestle Maniacs", it is shown that he carries a spare wrestling outfit around in the van.
Darker and Edgier: Certain episodes, at least. The backstory for the two ghost brothers in "Big Scare in the Big Easy", for instance, states that they killed one another in a duel in the family graveyard. The provided flashback shows the two brothers loading their pistols on-screen, and ends with the sound of a gunshot.
Demoted to Extra: Scooby-Doo himself, in most cases, and sometimes Shaggy. Typically the show would shift focus onto Fred, Daphne and Velma, but one major exception was the episode '"Camp Comeoniniwannascareya", which did not feature Fred, Velma or Daphne at all; it just featured Shaggy and Scooby-Doo as the main characters.
Everybody Did It: In one episode it's shown that all the suspects were in on the plan.
Precious Puppies: The Secret Six are a group of six golden retriever puppies that appear in several episodes. And they are adorable, especially when they're performing military exercises.
Farmer's Daughter: Velma's cousin Marcy is one of these, but without the overly protective father.
Food As Bribe: How the gang usually persuade Shaggy and Scooby to be monster bait. In one episode, they use Scooby Snacks to persuade Shaggy and Scooby to be literal bait—the two end up dressing like octopi.
Former Child Star: The Mystery Machine used to belong to the Mystery Kids, a musical group that starred a brother and a sister. They appear in the episode "It's Mean, It's Green, It's the Mystery Machine", where their mother has been attempting to arrange a return to stardom for them. They decide at the end that they're happier being nobodies.
Genre Savvy: In one episode, Shaggy and Scooby brought their own Scooby Snacks so they'd not have to accept the ones the gang offered as bribe. The gang reacted by offering milk, which they accepted.
This show is often genre savvy a LOT; every episode has to parody the classic Scooby-Doo formula in some way.
Human Popsicle: Dr. Armind Zola attempts to enact this trope in "Uncle Scooby and Antarctica".
Inexplicably Identical Individuals: All Daphne needs to look identical to her cousin Danica is a wig. She says that her Uncle Julius also resembles Danica when he wears heels.
Velma looks like her cousin Marcy's parents, especially in contrast to Marcy herself, ironically.
It Was a Dark and Stormy Night: Surprisingly only done on ONE episode: "The Vampire Strikes Back," it starts off as your classic Scooby-Doo thunderstorm (complete with crackles, pops and vinyl hiss on the first couple of lightning flashes), but then it gets more realistic and LOUD, and then after the loudest thunder crash of them all (when Fred leaps down from a tower to save Daphne near the end), the storm abruptly comes to an end.
Lampshade Hanging: And lots of it, too. Every episode had to have at least one or two parodies of the classic Scooby-Doo conventions, to the point where it was no longer funny.
Latex Perfection: Typically avoided in this series in favor of the villains using makeup, animatronics, holograms, etc. Though there are a few exceptions in this series, such as in the intro, and in "A Scooby-Doo Valentine" when the gang is framed by rubber-masked impostors, and Scooby is unmasked to reveal J.C. Chasez of N'Sync!
Let's Split Up, Gang: In pretty much every episode. The show does occasionally break the pattern of the two groups: Fred, Daphne and Velma in one group and Scooby and Shaggy in the other.
MacGyvering: It's not rare for Daphne to do this, usually with items she carries around in her purse.
The Minnesota Fats: One episode introduces a girl named Verona Dempsey who plays this to Velma (all while being really bitchy to her). It turns out she's one of the episode's two villains.
Monster Clown: A giant version of this attacks a mini golf course in "A Terrifying Round with a Menacing Metallic Clown". This is more of a problem than usual because Velma has a phobia of clowns.
Not Himself: In "E-Scream", everyone aside from Velma acts pretty weird, Fred doesn't want to split up, Daphne wears shoes that don't match, and Shaggy's catchphrase was slightly different*
Once an Episode: Nearly all the parodies of the old series (especially spoofing the "meddling kids" line.)
The Other Darrin: After Don Messick's death, Frank Welker took over the voice role of Scooby-Doo, in addition to voicing Fred as he always did, which resulted in Scooby-Doo sounding more like Brain from Inspector Gadget. Velma was also recast to Mindy Cohn, which made her sound more like Mandy from Grim and Evil (ironically, Mandy was voiced by Grey DeLisle, who was Daphne's voice actress since 2001).
Also, in The Vampire Strikes Back Kimberly Brooks did double-duty and voiced both Luna & Dusk of the Hex Girls (although the episode's credits claim that Dusk's usual actress, Jane Wiedlin, provided singing vocals).
Out-of-Character Moment: In-universe: In "E-Scream", this is what tips Velma off to the fact that she's in a virtual reality game: Freddy doesn't want to split up, Daphne is okay with wearing mismatched shoes, and Shaggy and Scooby are perfectly willing to be bait for a trap even without being offered Scooby Snacks. Shaggy saying "Toinks!" instead of "Zoinks" is just the final nail in the coffin.
Panty Shot: Velma in "It's Mean, It's Green, It's the Mystery Machine". But you've gotta not blink or you'll miss it.
One episode plays with it; the monster is real. It's just a creature that was disturbed by the crooked plan of the villain.
Ship Tease: There's some of this between Fred and Daphne, particularly in the Valentine's Day episode. They are the main Fan Preferred Couple, after all.
Shout Out: Wile E Coyote And The Road Runner both make a surprise cameo appearance at the beginning of "New Mexico, Old Monster", complete with their classic designs and the appropriate sound effects.
Totem Pole Trench: In the episode "Gentlemen, Start Your Monsters", Jimmy and his sister Cindy wore a jumpsuit, with one on the other's shoulders.
Wacky Racing: Fred enters the Mystery Machine in one of these in the episode "The Fast and the Wormious". Because this is Scooby-Doo, the already bizarre race gets interrupted by a large worm monster, which turns out to be one of the racers.
With Friends Like These: Fred, Daphne, and Velma could be so mean to Shaggy and Scooby sometimes.
You Meddling Kids: Parodied in nearly every episode as well; instances include having twin villains say it in unison (in "The Vampire Strikes Back") and a young kid calling the gang "meddling grownups" (in "Gentlemen, Start Your Monsters"). And the villain of "There's no Business Like Snow Business" called them "meddling teenagers".