The film starts with Shaggy in the ER, screaming loudly without catching a breath. The doctor is so amazed by this that he wonders if it's a violation of the laws of physics.
How does the doctor cure Shaggy? He simply walks up to him and yells "Hey! Stop screaming!" And it works.
Daphne: Why didn't that work when he tried it?
Doctor: Eh, people listen to doctors.
When the doctor tells the gang that Scooby can't be in the ER, Daphne says that Scooby is a certified medical rescue dog, and pulls out a license to prove it. But the doctor doesn't buy it, and believes that Daphne just made the license in Photoshop. Daphne denies this. And then says that Velma did it.
Everything to do with Shaky Joe.
Shaggy: Hey, Shaky Joe, what do you do for fun?
Shaky Joe: I KNIT.
[holds up a tangled mess of thread]
Shaky Joe: IT'S A SCARF.
Scooby trying coffee for the first time. Highlights include him jumping up and down on Shaggy's head, pouncing on Fred when he enters the cafe, and running around ''on the ceiling."
Whenever someone says Shaggy's keyword (bad), be prepared to laugh.
Fred: Shaggy, what are you doing?
Shaggy: Saving your butt, Jones. Get used to it!
When Shaggy is in the middle of his awesome stunt to escape the mines, Daphne triggers the keyword that causes him to turn back into a coward. Eventually Fred motivates Shaggy enough to have him try to jump to the ledge he needs to get to, but he needs Fred to give him a movie line first.
Fred: ... How about, 'when you say jump, I say how high?'
Shaggy: Fred, that doesn't make any sense!
The G.P.S. from Abracadabra Doo makes the gang stop at a tattoo parlor.
The snarky owner of the buffet restaurant, who has a remarkably quick grasp on when things are going to get bad.
Owner:[after Shaggy and Scooby eat half the buffet in one sitting then go for seconds] So... do I file for bankruptcy now or...
And later, when the biker gang shows up.
Shaggy: Like, those guys aren't going to get out of control are they?
Owner: I think they'll be okay as long as no one does anything to aggravate them.
[Shaggy accidentally hits one of them in the face with his plate]
Owner: Like... that, for instance.
Lovestruck Velma. Especially the part where she spends an entire conversation with Winsor in such a monosyllabic lovestruck daze that he thinks she's not really listening at the end.
Velma and Winsor spend over a minute in a Held Gaze. Fred loudly clears his throat. Velma throws him a bottle of cough drops without taking her eyes off of Winsor at all.
Daphne's been riding a motorcycle since she was five. Complete with Cutaway Gag.
Fred: Isn't it illegal for a five year old to ride a motorcycle?
When Shaggy's trying to lead the gang out of the cave:
Svankmajor: ... Shaggy, you'd better hurry.
Shaggy: I was born hurried.
Fred: Is that part of the brave thing when you say weird stuff that sounds like movie lines?
Shaggy: Yes. Yes it is, big guy.
Fred: Well, alright then.
When Scooby-Doo finds a rare dinosaur bone, Professor Svankmajor thanks him and Shaggy for their significant contribution to Paleontology.
Shaggy: The study of pale things?
"This can go two ways, punk. One: you walk away. Two: I walk on your face."
"I've got a plan. On the count of three, you invent a time machine. One, two-"
*completely nonchalant* "Aaaaannd..." *sound of dribbling water* "theeerree goes the bladder..."
The point where Mr. Hubley gets out from his hiding place after the gang follows the raptors into town. He finds the food replicas that Scooby and Shaggy built of themselves, and thinks it's the real them.
Mr. Hubley: Scooby! Shazzy! No, they were so young!
"If there's one thing I can't stand, it's ghost dinosaurs!"