Muppet Treasure Island/Funny

Virtually the entire movie in one way or another.
When Gonzo spills gunpowder all over the store room floor at the Admiral Benbow, and then the pirates attack him and Rizzo; they drop a lit candle onto the spilled gunpowder, with awesome and hilarious results.
"He's dead? I thought this was supposed to be a kids movie!"
"...and people die by falling overboard!" Great line to insert in a cheery song about sailing for adventure.
Hearing that pirates are superstitious, Bunsen thinks up a way to get Silver's pirate crew to leave. Sam rises out into the ship's platform in white flour, with a deadpan performance as a 'ghost': "Boogie, boogie, boogie. I am the ghost of Samuel Arrow." *beat* "Boogie!" Followed by the entire pirate crew throwing themselves off the ship in panic.
In the middle of Kermit's Flynning, Silver says "Excuse me", and a distracted Kermit lets the sword go flying. Made better by the look of "you've gotta be kidding me" on Curry's face.
The Swedish Chef's very random appearance (complete with a pig snout) as the tribe's chef. The veggies says what the audience is thinking.

Vegetable: Well, how else were we gonna get him into this movie?

"Very good. *eye roll* You're forgiven."
The roll call scene.

Samuel Arrow: Big-fat-Ugly-bug-faced-baby-eating-O'Brien?"
Woman (with a deep voice): Aye.

- Pretty much every single name called is a gag.

Arrow: Old Tom!
Old Tom: Here!
Arrow: Really Old Tom!
Older Tom: Here!
Arrow: ... Dead Tom!
Dead Tom: *a living Muppet skeleton steps into frame* Here!
Arrow and Smallett exchange looks as if saying "what do you know about that!"

The "Cabin Fever" number.
This exchange:

"Dead Tom's dead! Long John shot him!"
"But--Dead Tom's always been dead. That's why he's called 'Dead Tom.'"
"Oh." (drops the bones)

- And Long John rolling his eyes in the background.
- And this one:

Long John: The Black Spot? You dare to give me the Black Spot?
Clueless Morgan: (fearful and quickly points at Polly Lobster) He told me too!
Polly: Shut up, will ya!
Long John: And it's drawn on a page from the Bible? You tore a page from the Holy Scriptures to make a pirate’s death sentence?
(Crowd parts to show Mad Monty holding said bible. He quickly tries to get rid of it)

After the roll is called and Kermit (and the audience) get a good look at the rather unsavoury crew, he very calmly and politely asks to see the main characters in his cabin. Cut to him screaming "WHO HIRED THIS CREW? THIS IS UNDOUBTEDLY THE SEEDIEST BUNCH OF VILLAINS, CUTTHROATS AND SCOUNDRELS I EVER LAID EYES ON SO WHO HIRED THEM?!?!?
- "Your finger hired the crew???"
- "No, that's silly! That man who lives in my finger hired the crew."
- "A cook, and a guy who lives in a bear's finger???"
- "I'm beginning to worry about this voyage."