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.
After Shaggy and Scooby accidentally bring all the costumes back 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 a monster that they're not afraid of: the Cotton Candy Glob. The monster's Oh Crap! is completely understandable.
Cotton Candy Glob: NO! I'LL GIVE YOU CAVITIES!
Later, when the others are looking for Shaggy and Scooby, the two come down the elevator, covered in the remains.
Shaggy: I wonder if there's a Two-Liter Soda Glob around here somewhere!
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 the Tasmanian Devil, a woman, and finally Scooby becoming super-intelligent and Shaggy becoming muscular.
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.
And then at the end of the same scene, after the team begin to suspect Jeremiah Wickles:
Shaggy: Precisely! (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."
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.