Are there any allegorical instances in Lord of the Flies?
I suppose the story behind LOTF is an allegory although I personally prefer my allegories to be more abstract in thought (like Animal Farm or Aesop's Fables). I'm sure there are several who disagree with me (see the attached link!).
I can buy into the ideas of LOTF being a political or religious allegory, but I really think it's a theme novel instead. My belief is that this novel isn't really symbolic of anything (the basic necessity of an allegorical tale); I think it's representative of human nature. The purpose of Golding's work wasn't for us to gain a deeper understanding of something through various symbols, it was to gain a deeper understanding of ourselves through truth. All of us can picture people who we know that could "fit the bill" for Jack, Ralph, Piggy, Simon, etc. That knowledge of real people makes us understand that the ideas of LOTF aren't symbolic, they're real.
An allegory is where something represents itself and also something beyond itself at the same time. For example, in the play Everyman the main character is himself and all of humanity simultaneously.
In LOTF, several of the characters, I think, do represent themselves and something larger. For instance, Piggy is a boy and he represents the thinking/logical part of humanity as a whole. He is reason.
Simon is himself, but he represents the innocence of humanity. He is the basic good.
Both of these characters and what they represent on the island are murdered by the darker forces of the boys.