- Virtually the entire movie in one way or another.
- Blind Pew the "Visually challenged" fiend, spends a majority of his scenes making one Blind Mistake after another; HE thinks a living moose head is Billy Bones, and during the pirates' raid on the Admiral Benbow, he opens a clock's case, rushes in, and bangs his head on the pendelum. When the inn is on fire, and everyone else is panicking, all Pew says is, "I think I smell something burning, no?"
- Samual Arrow is still not done gaging the lifeboat's seaworthiness as he rows ashore, as he then asks the others to join him in the "exceptionally safe" lifeboat.
- 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? And this was supposed to be a kids movie!"
- "We're standing in a room with A DEAD GUY!!! (they all freak out)
- Billy Bones's last words "Beware of running with scissors or any other pointy objects, it's all good fun until somebody loses an EYE!! *dies*
- "...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.
- Just the way he said, "Excuse me," made me laugh.
- Arrow's reaction. He face palms...while punching Polly Lobster without even looking.
- The Swedish Chef's very random appearance (complete with a fake 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?
Samuel Arrow: Angel Marie!
- Pretty much every single name called is a gag.
Arrow: Old Tom!
Old Tom: Aye!
Arrow: Real Old Tom!
Older Tom: Aye!
Arrow: Dead Tom!
Dead Tom: *a Muppet skeleton steps into frame, manipulated by another Muppet* Aye-aye!
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?!?!? *huff* *huff*" Everyone points to Fozzie, who points at his own finger.
"Your finger hired the crew???"
"No, that's silly! That man who lives in my finger hired the crew. Mr Bimble. He's very smart. He's been to the moon." *listens to his finger* "Thank you. Twice!"
"A cook, and a guy who lives in a bear's finger???"
"I'm beginning to worry about this voyage."
- Benjamina's spoiled entrance. "You stupid anteater!"
- Statler and Waldorf are the ship figurines in this movie, and in their last appearance, they save Kermit and Ms. Piggy.
Statler: Waldorf you old fool. We're heroes! We saved the pig and the frog.
Waldorf: Well, it was too late to save the movie. (All laugh)
- The... "showdown" between the pirates and pig islanders.
You! Tiny pirate men stand down, or die like stinking dogs!
* Long John shoots his headdress off* Chieftain:
We see you have boom-boom sticks. *beat* Bye bye.
* tribe runs away*
- Clueless Morgan and company trying to torture Gonzo for information. They put Gonzo on the rack, but the only thing they succeed at doing is making his arms and legs ten feet long.
Gonzo: I might even have a future in the NBA!
- Even funnier in that if you watch the scene closely one of Gonzo's arms or legs gets over to where Smallet is standing and starts tickling him while Smallet stares into the camera.
- The following exchange as Gonzo and Rizzo sit eating apples:
Gonzo: This feels so weird.
Rizzo: What? That Mr. Arrow's dead?
Gonzo: That, and my pants are filled with starfish.
Rizzo: (beat) You and your hobbies.
- Made even better in the film's climax when Gonzo whips out said starfish to use as ninja stars against one of the pirates.
- Statler and Waldorf's first exchange:
Statler: Take a cruise, you said. See the world, you said. Now, we're stuck on the front of this stupid ship.
Waldorf: Well, it could be worse. We could be stuck in the audience.
- This dialogue when Polly Lobster is introduced:
Gonzo: I thought sailors had talking parrots as pets.
Long John Silver: Talking...parrots?
- One of the best bits in the film comes near the beginning as the Bimbo's patrons are leaving:
Mrs. Bluveridge: "Be sure to be back tomorrow for our weekly special: roast suckling..."
(a group of pigs look scandalized)
(The pigs are mollified. Then a very offended potato-woman walks by)
Mrs. Bluveridge: "No offense, deary."