These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Hilarious in Hindsight: The Lamanites utterly fail to take the city of Noah and the narrative describes how some of the Nephites were only wounded due to arrows striking their legs. No doubt more than one of them took an arrow in the knee.
Tearjerker: The final chapter, when Moroni is the Last of His Kind. All the time he is writing, he is completely alone, his father has been killed, and he's doing all he can do to finish his work while on the run. He knows full well that God will quit protecting him after he finishes, and he wants it to be this way, as he has nothing else to live for. The last verse is him saying goodbye to the reader and hoping to see them in the afterlife.
Fridge Brilliance: You'll notice that there's no cursing for the first twenty minutes or so of the play until they finally arrive in Africa during "Hasa Diga Eebowai". That's to lull the viewer into forgetting that they're watching a show written by the creators of South Park and then club you over the head with as much cursing as humanly possible.
Fridge Horror: Elder McKinley's situation, when you remember the Ugandan government's general attitude towards homosexuality.
At one point Elder Cunningham calls Nabulungi Nala; in the current Los Angeles show Nabulungi's actress played Nala and General Butt Fucking Naked was Mufasa.
Andrew Rannells (the original Elder Price) coming out as gay.
Magnum Opus: Some consider this to be the all-time best work from Trey Parker and Matt Stone. Considering that it won nine Tony Awards, and is one of their most successful works financially, it is easy to see why.
It also helps that the musical never portrays Mormons or even Mormonism itself as bad. The whole point of the musical is that religion can be used to bring people together, and that's what the Mormons ultimately do.
During the touring production, not only has the LDS church bought multiple ads in the Playbill, but they station missionaries at the entrance to hand out cards. Protesting isn't going to work, so why not use it to their advantage?