Adaptational Attractiveness: Most noticeably with Velma - who is given a cute face and an attractive figure here (whereas her original design had her be very plain and slightly overweight) - and to a lesser extent Shaggy, who probably benefits more from the less rough art-style.
Anti-Villain: Used several times, a first for the franchise. Every once in a while, the characters would run into a villain with sympathetic motives - generally, these folks would be let off because "nobody got hurt" (though not for lack of trying, sometimes) or the case just dropped without fanfare.
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 (resembling a show produced by Adelaide Productions, such as Men In Black and Jackie Chan Adventures). It hits some characters more strongly than others, like Velma's totally redesigned body shape.
Back Blocking: In "Big Appetite in Little Tokyo". When a bunch of angry Japanese villagers are crowding around the gang, one of them in a light grey shirt fills the screen.
Berserk Button: In Fright House of a Lighthouse, 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, brunette Velma and Velma's blonde cousin, Marcy.
Clothes Make the Legend: While the Scooby Gang's outfits have been modernized (save for Velma, for some reason), they retain the same classic color scheme, independent of what they wear (except for disguises): Fred's is always white and blue, Daphne is always wearing purple and magenta, and Shaggy always wears green shirts and burgundy pants (Velma's orange-on-red scheme is retained as well for other types of clothes). It borders on Limited Wardrobe.
There are actually two subtle changes on Velma's design: her shoes now have platform heels and her skirt is no longer pleated all the way around.
Continuity Nod: 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.
Dinner Order Flub: In "Pompeii and Circumstance", Fred is continually misreading his Italian phrase book. As a result, he orders a potted plant at a restaurant.
When you look at it, Daphne (being much more fashion-conscious than before - even though she's still sharper than Fred, and still more competent than she was in the original series) and Velma (who must always be right and, whenever she's wrong, the script will find a way to prove her right at the end of the day...with a few notable exceptions) qualify as well.
When Scooby and Shaggy enter a scene, you know the first thing they'll say will be food-oriented. Then again, it isn't really that different from their other portrayals.
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.
Even when Shaggy and Scooby see this coming, the gang manages to work around it. See the Genre Savvy entry.
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.
Gender Misdirection: The gang once went to an amusement park without knowing anything about its owners than their names (Chris and Terry) and their fame obtained by building the park's rides. The gang (mostly Shaggy) expected Chris and Terry to be men but it turns out they're girls.
Gentle Giant: The "Coral Creature", which turned out to be one of the few (if not only) times where the monster was real.
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.
Getting Crap Past the Radar: In "A Scooby-Doo Halloween", Velma's cousin Marcy says that she's turning 18, "Able to legally... vote." While giving Fred a flirtatious look that would've been toeing the line on its own.
Human Popsicle: Dr. Armind Zola attempts to enact this trope in "Uncle Scooby and Antarctica".
Ink-Suit Actor: Brett Hull, Mike Piazza and skateboarders Chris Klug and Ryan Sheckler are among the celebrities to appear on the show in cartoon form. In "A Scooby Doo Valentine," the perps who disguised themselves as the gang are unmasked to be caricatures of their voice actors — Frank Welker (Fred), Casey Kasem (Shaggy), Grey DeLisle (Daphne) and Mindy Cohn (Velma).
One-shot character Mr. Wackypants ("Riva Ras Regas") greatly resembles his voice actor, Rip Taylor.
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 (as seen in the trope page) to reveal J.C. Chasez of *NSYNC!
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.
Mythology Gag: The flashback scene of Velma's birthday party in "A Terrifying Round With A Menacing Metallic Clown" is designed in the style of A Pup Named Scooby-Doo. It explains Velma's fear of clowns—the clown hired for her party destroyed her prize gift, a set of encyclopedias, and it made Velma run off crying.
The episode Simple Plan and the Invisible Madman pays homage to The New Scooby-Doo Movies, where celebrity guest stars in animated form helped the gang solve cases.
Not Himself / 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.
Shaggy's bravery in "A Terrifying Round with a Menacing Metallic Clown" could count as well, if only because he didn't want a monster stopping him from winning the mini-golf tournament. In the same episode, Velma goes off cowering with Scooby as her childhood fear of clowns comes to the surface.
Notzilla: An episode has a giant monster named "Shagzilla". He's supposed to be Shaggy cursed to transform into a Godzilla parody at night (Actually, it's a giant robot built by the villain of the week, and Shaggy is duped into believing he really is the monster because, while he is asleep, he is made up as the monster and placed on a Tokyo maquette.).
Obfuscating Disability: Invoked in one episode, by our villain of the day, Avalanche Anderson, to prevent anyone from knowing that he was behind the Snow Creature.
Once an Episode: Nearly all the parodies of the old series (especially spoofing the "meddling kids" line.)
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. (For the record, they're white as opposed to matching her skirt color as before.)
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.
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.
Uncanny Family Resemblance: 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.
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.
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 in "Gold Paw", the villain refers to them as "interloping adolescents". And the villain of "There's no Business Like Snow Business" called them "meddling teenagers".
You Must Be This Tall To Ride: The episode "Roller Ghoster Ride" featured a few scenes that had a young boy being told that he was too short to go on certain rides, such as the Sky-Diving Simulator, the Slingshot, and the Rocket Coaster. Also, he was ruled out as a suspect for being too short for the costume. In the end, after the villain of the episode was caught, the boy gets to ride with Shaggy and Scooby on the food-based ride that was built for the amusement park.
Younger and Hipper: Basically, this is the original 1960s show retooled for the 21st century, complete with more modern and realistic settings, situations and sound effects, and a poppy punk soundtrack (included the reworked main theme by Simple Plan).