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.
Angel/Devil Shipping: Ralph and Jack. Ralph represents the civil, sane, moral part of the human mind, while Jack represents the basic, primal instincts, the darkest, most savage part. Their looks also suggest it, Ralph being blond-haired, while Jack is described to be with red hair.
Also, Simon/Roger, with Simon being one of the most innocent children on the island, while Roger is one of the most savage ones.
Anvilicious: The book goes about preaching its message with the subtlety of a Rhino in heat.
Some have read it as a slightly friendlier Aesop against the racial stereotypes of the era, showing that under the wrong circumstances even British schoolboys fall into savagery just as easily as any "inferior" cultures.
Fanfic Fuel: None of the boys' pasts is revealed in the book (except for some details about Ralph and Piggy), nor is their fate after the island.
Fan-Preferred Couple: Fanfiction and fanart seem to prefer Jack/Ralph (Jalph) most of the time, even though there is fanwork with other couples too, like Roger/Simon, Jack/Roger and Ralph/Simon.
Foe Yay: Quite a lot, between Jack and Ralph. One particular quote: Now it was Ralph's turn to flush but he spoke despairingly [...] "Why do you hate me?" The boys stirred uneasily, as though something indecent had been said. The silence lengthened.
Inferred Holocaust: The navy shows up at the end to rescue the boys. It seems like a happy ending... until you remember that a nuclear war had been going on at the start of the book, which means that Britain (and the rest of the world) is most likely in a sorry state. Not exactly the best thing to come home to after struggling for survival on a remote island.
Moral Event Horizon: The frenzied, hysterical killing of Simon by Jack and the other boys comes dangerously close to it. It's finally crossed (and in a very symbolic way) when Roger pushes a massive boulder down on Piggy, sending him flying off the cliff and to his death.
Oddly enough, the killing of a sow, with metaphors to make it sound like gang rape, is supposed to be the first indication the horizon has been crossed, or was about to be crossed pretty soon.
In the 90s film as well. Especially the way Ralph screams "NOOOOO!"before he gets killed, and that deadpan pause after his head gets crushed.
The tribal dance around the fire in the second movie. The gratuitous slow motion didn't help, either.
Let's not forget that, with no dialog, the Lord's big scene in the '60s movie becomes, essentially, Simon having a Staring Contest with the head.
One-Scene Wonder: The titular Lord of the Flies only appears at the end of chapter eight. However it has an amazing impact and is probably one of the best scenes in the book, showing that Tropes Are Not Bad.
OTP: Jack/Ralph is for those who like a love/hate romance. Ralph/Simon for those who love a cute, wholesome romance. Jack/Roger for those who are into a psycho romance between two psychos.
Values Dissonance: The 63' film had prepubescent nudity. It was completely non-sexual and realistic, but because of the Pædo Hunt, modern audiences are met with shock and disgust at the film showing young boys' boy parts.
"Weird Al" Effect: Far fewer people remember the works (such as Two Years Vacation and Coral Island) that Lord of the Flies was parodying than they do Lord of the Flies itself. The fact that it was a Deconstructive Parody is also not well-known.
What an Idiot: Piggy telling Ralph about a nickname he doesn't want to be called.
Piggy. He actually hates that nickname, but even Ralph insists on calling him that. We never learn his actual name. Plus he's asthmatic, nearsighted, and almost only valued because his glasses help create the fire. While he may be a Non-Action Guy, he (unlike Ralph) actually does Dare to Be Badass and confronts Jack and his vicious tribe. A pity it didn't save his life...