* Johnathan Jacobo's escape from prison via winged harness.
--> '''Jacobo''': Ahaha! So long, suckers!
--> (Wing harness begins to fall out of sky)
--> '''Jacobo''': [[OhCrap HELP ME SUCKERS!]]
** Becomes a BrickJoke; [[spoiler:Jacobo turned out to be alive at the end of the film (implying that his machine actually worked). During the DancePartyEnding, 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 OhCrap 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, [[BigEater naturally]], begin sampling their contents. HilarityEnsues as they transform into all manner of things, including [[WesternAnimation/LooneyTunes 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.
--> Shaggy: Ah...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.
* Velma performing a GroinAttack on the Black Knight is oddly amusing. Doubles as CrowningMomentOfAwesome.