When Elders Price and Cunningham are waiting for their plane, an African sunset backdrop suddenly falls while a woman dressed in a Lion-King style costume leaps out and sings an Expy of the opening vocals to The Circle of Life. The curtain then drops to reveal it was just a surprise to send the boys off to Africa
From "All American Prophet", in the middle of the song...
Elder Price: Even though people wanted to see the golden plates, Joseph never showed em....
Doctor:(in a deep, operatic voice) I haveeeee maggots in my scrotummmm! [beat]
Elder Price: Uh, okay. Well anyways.....
Joseph Smith and the Mormons boogying it up in the background while Elder Price sings also qualifies.
Pretty much all of Elder McKinley's lines in "Turn it Off", but in particular:
Elder McKinley: Imagine that your brain is made of tiny boxes, then find the box that's gay and CRUSH IT! Okay?
Another stand-out of 'Turn It Off'? In the stage performance, the part where they start clapping literally makes the lights go out, plunging the stage into total darkness for a couple of seconds. The second time this happens, when the light comes back up, they're all now wearing sparkly, hot pink vests on-top of their normal clothes. Elder Price looks totally confused for a second, before deciding to go along with it.
The SMHD costumes alone are hysterical, from Halloween-style devil outfits with plastic pitchforks to maple doughnut hats to demons wearing giant coffee cups (who torture Kevin by force-feeding him coffee) to sparkly black top hats and waistcoats.
Elder McKinley, again, after waking Elder Price from the Spooky Mormon Hell Dream:
Elder McKinley: You had the Mormon Hell Dream? Was I in it?!
"I Believe" is a funny enough song as is. The fact that Elder Price is practically prancing up to a maniacal warlord and grabbing his hand, however, makes it priceless - the only reason that the General's men aren't shooting him is because they're too confused by what's going on.
General: ...The fuck is this?
"I believe... that in 1978 God changed his mind about black people!" (followed by the choir echoing "black people!").
Elder Price, after having the Book of Mormon shoved up his ass, gets completely wasted...on coffee.
Which becomes a bit of Fridge Brilliance, when you realize that Elder Price is purposely trying to avoid sleeping at all costs, hence the coffee.
Elder Price: Well, if it isn't Elder Cunningham! The super-mormon!
This is followed up by his monologue on why he became such a devout Mormon. He hoped that when he died, he'd get his own PLANET ORLANDO!
From "Baptize Me": I'M WET WITH SALVAAATIOOON!!!
It's hard to describe "Joseph Smith American Moses", but... "Joseph Smith, magical AIDS frog! Brigham Young, frog on his clit face!"
"Compassion! Courtesy! Let's be really fucking polite to everyone!"
The costumes and choreography.
Also, the summation at the end of the song: "Joseph Smith, AIDS frog; Brigham Young, clit face; Shit come out the butt; Jesus says 'fuck, fuck,' Mormons!"
The ending with the Ugandan Elders. "Hello, my name is Elder Matumbo..."
"Hello, my name is Elder Butt Fucking Naked."
"And if you put that gun down I will—oh, okay, I'll leave!"