Jonathan Jacobo's escape from prison via winged harness.
Jacobo: Ahaha! So long, suckers! [Wing harness begins to fall out of sky] Jacobo:HELP ME, SUCKERS!
Becomes a Brick Joke; Jacobo turned out to be alive at the end of the film (implying that his machine actually worked). During the Dance Party Ending, he's seen trying it again.
Shaggy: Wickles has led us to, like, a terrifying ghost town! Scooby: Roast town? Shaggy: Yes, a ghost town! Scooby:[beat]RHOOOOOOOOST!!! [Wickles turns and glares at the "shrubbery"] Wickles:Darn bushes yowlin' at me again. [continues walking]
After Shaggy and Scooby accidentally bring all the costumes to life while messing with the control panel:
Shaggy: We have... to remain... calm. Scooby:[screams in fear] Shaggy:CALM, SCOOBY-DOO!YOU'RE NOT BEING CALM!!! Scooby:[slaps him] Shaggy: I needed that! Scooby:[slaps him again] Shaggy: I needed that, too! Scooby:[punches him] Shaggy:You're pushing your luck, Scoob!
When Shaggy and Scooby encounter the Cotton Candy Glob. They're initially scared like normal, but once the monster announces its name, they gradually both bear the most wicked excited looks, realizing they can literally just eat it. The monster's Oh, Crap! is completely understandable.
Later, when the others are looking for Shaggy and Scooby, the two come down the elevator, covered in the remains with Scooby wearing the cotton candy cone as a hat.
Shaggy: Like, this is the greatest day of our lives! Finally, a monster we can sink our teeth into! Y'know, Scoob, I'm kinda thirsty. I wonder if there's a Liter-Sized Soda Glob anywhere.
Shaggy when the gang finally park by Wickles' mansion.
Shaggy: Oh, man. Another creepy crib. How come we can't ever investigate, like, a Burger King or something?
While exploring the Monster Hive, Shaggy and Scooby come across a fridge full of flasks and, naturally, begin sampling their contents. Hilarity Ensues as they transform into all manner of things, including Scooby turning into a monster and then the Tasmanian Devil(in 2D cartoon form), Shaggy's body turning into a woman's, and finally Scooby becoming super-intelligent and Shaggy becoming muscular.
Also, Scooby's rant upon completing his transformation into a genius with Einstein-like hair:
"My... GOD! It seems as if I've become... [rapidly sorts through the chemicals in the fridge and takes two of them] ludicrously intelligent, haha! It's awful![Begins mixing the two chemicals as they change colors] Oh, how I long for the blissful ignorance of my former self; [tosses a flask to pluck a hair off his head and add it to the other] chasing cats, licking my rear end, [catches descending flask] eating my own vomit - oh, those were wonderful times!"
Scooby and Shaggy are trying to be better detectives, and Velma just printed out a clue. Shaggy snatches it out of her hand.
Shaggy: Alas, what are these strange markings? Fred:[turning the paper right side up] Words. Shaggy: Ah... words.
And then at the end of the same scene, after the team begin to suspect Jeremiah Wickles:
Shaggy: Right! [everyone turns round to look at him] Uhh... [turns to Scooby] Scooby-Doo! What's your conclusion? [Scooby turns his notepad around to reveal a drawing of a rabbit] Scooby: Bunny! [moves the notepad around to make it look like the rabbit is hopping]
"They're totally having a montage in there without us."
Immediately following that is a poignant moment where Shaggy is skipping stones and lamenting that he and Scooby only ever help by accident with their bumbling. He just wants to do the right thing on purpose once, and he skips another stone only to hear a metal clunk. His reaction shows that if he and Scooby ever did one thing right, it was sound the alarm:
"Capcutler's ghost... Captain... Cutler's...! GHOOOOOOOOOST!!!" (Running back to the clubhouse) Captain Cutler's Ghost!"
While being chased by the monsters:
Shaggy: This is tied for the most terrifying day of my life! Velma: Tied with what? Shaggy: EVERY OTHER FREAKING DAY OF MY LIFE!
The Pterodactyl Ghost's expression when Shaggy and Scooby fail to capture it, as if thinking "Did you really think that would work on me?"
It has its arms folded and everything.
Velma performing a Groin Attack on the Black Knight is oddly amusing. Doubles as Moment of Awesome as the Black Knight is made of iron and all she has is a small, orange shoe. What are her feet made of?
Fred: "And the real identity of Ned is... [pulls on hair] ...Ned!"
The gang gets trapped at the Wickles Manor. When their ball-cage comes to a stop they're greeted by the previous uninvited guests: a pair of Mormons spreading the good word, and a Girl Scout selling cookies.
Girl Scout: Hey... you wanna buy a box of cookies? Mormon: Excuse me, have you heard the Good News? Scooby:Yeah, there's cookies!
What makes the scene even funnier is Shaggy, one of the most iconic Big Eaters in all of fiction, giving the Girl Scout a look that plainly says, "This really isn't the time and place!"
Notably, this doesn't last long. Once they've been freed, Shaggy can be seen with a box of cookies, and the Girl Scout is counting a massive wad of cash. She's so busy counting she almost doesn't hear Scooby thank her for the cookies.
Shaggy trying to non-verbally explain to Scooby that his wig is slipping off when they're incognito at the Faux Ghost and Scooby misinterpreting his gestures as a dance move.
After the attack at the museum early in the film (where most of the exhibits are destroyed), there's a brief Visual Gag of the damaged skeleton ghost costumes outlined in chalk like a murder scene.
Fred's slip-up when he deals with Heather Jasper Howe.
Fred: You're doing that thing again where you take everything I say out of context. You're trying to make it look like I think Coolsville sucks! (realizes he's on camera)No! Don't record that![runs off]
Sure enough, he's taken out of context once again:
Heather: All Fred Jones had to say was... Fred: I think Coolsville sucks! (Fred bangs his head against the steering wheel)
Velma flirting with Patrick while wearing the Spy Catsuit, particularly when she leans towards him and the outfit makes a fart-like squeaking sound. She swears that it's the outfit, and Patrick seems to believe her. She leans in again, only for her to then fart for real.
Shaggy sticking his head inside a phonograph causing it to explode. Even funnier, the song it starts playing is "Baby Got Back" by Sir-Mix-A-Lot.
Phonograph: I like big butts and I cannot lie! You other brothers can't deny! When a girl— [Shaggy turns it off while coughing after he puts his head in the machine that exploded]
"We're gonna die!" "Think positive!" "We're gonna die quickly!"
As the Big Bad is arrested, he and Wickles get into a shouting match about how Jacobo used to steal Wickles' tater tots and competed with him for the lead in My Fair Lady.
Velma trying to hide from Patrick when he comes to Mystery Inc.'s place to ask her out on a date. She and Daphne have a conversation on their hands and knees in her office.
When Shaggy and Scooby pose as fans of the costumed criminals to spy on Wickles, their former enemy expresses sympathy for Scooby's abnormally large nose.
When Jacobo and Ned are getting arrested:
Ned: You were a dude this whole time? Jacobo: Of course, dummkopf. Ned: But we cuddled!
It implies that Jacobo used the same gender bending potion that Shaggy drank to turn himself into a woman as part of his disguise as Heather Jasper Howe.
Shaggy and Scooby trying to barricade the door, only for the Black Knight ghost to waltz in from a secret passage behind them.
Shaggy: Thanks! Black Knight Ghost: You're welcome.. Shaggy:(Oh, Crap! expression)
