Elder Cunningham in "Man Up". He takes over the hero role of the show, kills a monster, and defeats Darth Vader while proclaiming that he's not his father. And the song is really catchy.
Elder Price near the end just blatantly saying, "You know what, guys? Fuck him." "Him" in this case refers to the Mission President, who just declared the Ugandan mission disbanded in failure and disgrace thanks to Elder Cunningham's embarrassing cavalcade of Ass Pulls.
The fact Matt & Trey can now be referred to as "Tony Award-winning Trey Parker & Matt Stone"
Matt and Trey are an Oscar away from having the coveted EGOT (Emmy, Grammy, Oscar, and Tony) quad-fecta because of The Book of Mormon.
The moment the villagers reveal they've always known Elder Cunningham's stories weren't real is a threefold moment of Awesome/Funny/Heartwarming. Funny because of their assertion that "Sal Tlay Ka Siti isn't an actual place." Awesome because the villagers aren't naive Funny Foreigner types being taken advantage of. They understand parables, metaphors, and the purpose of religion to instruct/inspire better than a lot of fundamentalists. Heartwarming because this instantly helps to restore Nabalungi's dying faith.
Elder Price singing "I Believe," a beautiful anthem about his faith. The lyrics clearly do poke fun at the absurd beliefs of a Mormon, but it's composed in such an uplifting manner that religious or not, you feel for him.
When Ammon decides to preach the gospel to the Lamanites, he goes to a Lamanite king, Lamoni, and asks for work. Lamoni puts him out tending sheep. Bandits scatter the sheep, and the rest of the shepherds panic, thinking that they're going to be executed. Ammon just goes to retrieve the sheep. Bandits come again the next day, and he cuts off their arms. The other shepherds bring the arms to the king, and Lamoni asks where he is. Turns out, he's still in the field tending the sheep as though nothing is wrong.
Helaman's 2,000 stripling warriors. They're a bunch of young men who answered the call to battle when the previous generation couldn't (they made a promise not to shed any more blood). So, when they actually get into battle, what happens? They defeat the enemy, and not a single one is killed.
When Samuel the Lamanite is standing on a wall, prophesying about the coming birth of the Savior, and calling out the Nephites on their behavior, some of them decide they don't want to take his words and shoot arrows at him. None of them hit him.
When Nephi is called on to recover the brass plates, he sneaks into the city and finds Laban (the current holder of the plates) passed out drunk. He then proceeds to chop off Laban's head, steal his clothing, and gets the man's servant to not only bring him the plates, but carry them to the edge of town in order to meet his brothers. After his identity is revealed, he persuades the servant to skip town and join them in their quest. The servant and his descendants later become loyal followers of Nephi and his descendants.