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.
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.