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Any instance where Guybrush uses the ventriloquism book to throw his voice in Part II, but of particular note is when he uses it on the monkey pirate captain and does a Captain Kirk impression:
Guybrush: (as LeChimp) I mean, take a look around, at me, at the rest of the crew... we're all monkeys. Mr. Fossey: You mean in the Darwinian sense, sir? Guybrush: No, I mean in the quite literal sense.
The reveal that Mr. Fossey's captain is not LeChuck but LeChimp, a mute, dopey looking gorilla modeled after Captain Kirk.
Guybrush: But If the captain is a gorilla, then that must mean Mr. Fossey is... Mr. Fossey: Aye aye, sir! Free bananas for the whole crew! Guybrush: (deadpan) ...an utter loon.
In the sequence where Guybrush fakes his death a second time to get buried in the Goodsoup crypt, hotel manager Griswold Goodsoup offers this gem:
Griswold: Oh, dear! He's had a sudden and completely unexpected relapse of death!
"You fool! You've given cheese to a lactose-intolerant volcano god!"
On that note, Lemonhead in general. "Shut up. Or I'll eat you."
Guybrush: Did I say "cannibal?" I, I meant to say... err, "cannon... ball." I want to be a cannon ball. BOOOOOM!
Lemonhead: ...You're not quite stable, are you?
Similarly, after the "human sacrifice" to the volcano god (which is actually a dummy made out of fruit), complete with dramatic ritual-saying and rope-cutting, the cannibals stand around the volcano's edge and toast marshmallows.
The "terrifying" shape of Skull Island.
Guybrush: That's a duck!
Lost Welshman: What are you talking about? Can't you see the skull?
Guybrush: This island doesn't look like a skull at all. It looks like a great big enormous duck. It should be called Duck Island!
Lost Welshman: Well, ya see... ya gotta squint and sorta turn your head and... ooooooooh! It's just so scary!
Guybrush: If you squint and turn your head it looks like a bunny.
Asking LeChuck what the real secret of Monkey Island is.
Stan's triumphant return. Especially if you've played the preceding games.
When entering Skull Island, Guybrush has the option of saying the out of nowhere line to King Andre: "Your Evil Plan will never work." Andre's reply: "But it is flawless. A series of carefully placed charges throughout Blood Island, all controlled by a series of satellites in Geo-sycnronis orbit, and only one man has the master switch. I am that man, Mr. Threepwood, and I —" and by that point he's cut off by Cruff, who has been trying to get him to not blurt out his Evil Plan for no reason the whole time.
Wally's fake beard.
Wally: Actually, it's a highly sophisticated beard weave made from the chest and back hair of real pirates!