Who the primary antagonist of the Scooby-Doo movie turns out to be. (It's Scrappy Doo.)
Really, every scene with the antagonist, which make him become so over-the-top obnoxious that it loops back around and becomes hilarious.
When Shaggy first mentions about how the others are important in the way of an interesting euphemism:
Shaggy: Hey you guys, look. I know I'm just the dude who carries the bags. But it seems to me we all play an important part in this group. I mean, we're just like a big, delicious banana split. Fred, you're the big banana. Daphne, you're the pastrami and bubble gum flavored ice cream and Velma, you're the sweet and sour mustard sauce that goes on top.
Shaggy: That sounds pretty good, doesn't it, Scoob?
Whilst flying to Spooky Island on the plane, Scooby (disguised as Shaggy's grandma) has to move to Fred and Velma due to Mary Jane having allergies to dogs whilst Shaggy and Mary Jane first meet. Then, Scooby sniffs at the scent of a passenger's cat and begins to bark at it, attracting everyone's attention.
Velma: Grandma? Fred: Velma, it's simple behavior modification. To cause a dog to discontinue any action, flick it on the nose. Observe. (to Scooby, who is next to him barking at the cat) Scoob? (Scooby turns and Fred flicks him on the nose) See? (However, Scooby socks Fred in the face and then chases after the cat.)
Afterwards, this line from Shaggy who he has to get Scooby under control as we only see the outside of the plane:
"Sit Grandma! Bad Grandma! Don't eat the kitty!"
Shaggy and Scooby taking some time to have a contest as to who can make the grossest bodily function noise, especially when Daphne walking in on Shaggy disco dancing to his own farts! So juvenile... but so hilarious! Made better when Scooby unsuccessfully tries to warn Shaggy about Daphne's presence, and then he gives a shrug at the camera.
All of the body-swapping scenes. The sheer absurdity of everyone's voices coming out of one-another's bodies and their cartoonishly over-the-top body language is hysterical. One moment in particular is Shaggy in Daphne's body, rubbing her belly and asking her in a tired voice "don't you ever eat?", implying that Daphne's anorexic.
Shaggy telling Daphne why they "Don't do castles". Bonus for Scooby acting everything out behind him, and glancing over his shoulder after Shaggy mentions being followed.
Shaggy: Because castles have paintings with eyes that watch you, suits of armor you think is a statue, and there's a guy that follows you every time you turn around! Daphne: How many times has that actually happened? Shaggy:Twelve. We're not gonna do it.
The short "instructional video" Fred and Velma find on how college kids should act, which depicts a hilariously hokey scenario about What NOT to do after having someone bump into you and spill your drink:
Nice Guy: Oh! Sorry, bro!
Angry Guy (as he breaks the glass with one hand): I will CRUSH YOUR BONES INTO DUST!
(Others stop and look in horror)
After Daphne kicks the door enough to open and then cheers herself;
Daphne: Oh yes! Oh yes! Oh yes!
[She dances around until she saw a cart about to hit her from behind]
Daphne: OH NO!!
Right before Shag and Scoob find out Fred and everyone around him are possessed, hes uncharacteristically talking to them in party lingo.
Shaggy: Like, what happened last night?
Possessed!Fred: Man, we got beats like it was the lizniz on earth, ya know what I'm sayin', G?
Shaggy: (nods, beat) No.
"It's time to summon the big muchachos!"
After Scrappy Rex says he needs Scooby's soul to complete his transformation, Scooby retorts, "Me? Don't you mean Melvin Doo?!"
The DVD Commentary has Sarah Michelle Gellar spend the entire scenario with the Luna Ghost pointing out which of the backsides on screen are actually hers and which are the stunt double's.
Linda Cardellini introduces herself by her name - Sarah Michelle Gellar corrects her to "Linda Edna Cardellini" and Linda goes "I am Linda Edna Cardellini" with exactly the same amount of stress on the middle name that Sarah did.
This exchange between Shaggy and Scooby when Scooby gets mad over Shaggy's attraction to Mary Jane is so shamelessly puerile it's hysterical.
Fred and Velma dance with the possessed people to blend in. But then Fred gets so caught up at the moment, he forgets to stop dancing at the end...until he sees the Oh, Crap! look on Velma's face and realizes all the possessed people are pointing at him!
Than he insists they should continue the dance.
Fred gets a bit defensive when Velma accuses him of shallow tastes.
Velma: All you care about are swimsuit models.
Fred: No! Hey, I'm a man of substance. Dorky chicks like you turn me on, too. (Velma just walks away in disgust. Fred is both confused and annoyed)
Fred: (to himself) It's a compliment...
Shaggy and Scooby meeting up with a possessed Fred
(Possessed) Fred: What up dawg? (sees Scooby) And uh, dog?
Scooby: Keepin' it real
The teaser trailer or Trailer Spoof where it is revealed that Scooby-Doo's shadow resembles Batman.
The ending where Shaggy and Scooby do what they do best: eat. In this case, challenging each other with entire glasses full of hot peppers. First Scooby has steam coming out of his ears, downing a whole jug of water, then repeatedly bashing his head with a tray before Shaggy pulls his tongue and cools it with ketchup. Then they both go for it, before it cuts to outside with twin trails of steam and lots of yelling.