physical or non-rational it succumbs, at least on the physical level. Whether its power is ever really extinguished (and here the parallels between Simon and Christ pertain) might provoke some interesting debate.

The Dead Pilot/The Naval Officer: the harmonizing of the three disparate forces within us; while it might be tempting to label this force "civilization," the fact that the novel's action unfolds in the aftermath of a war presumably waged at the behest of "civilization," such a label would need to be qualified.

It would be possible to interpret most of the other characters and objects in the story through this lens (e.g. the conch embodies the best qualities of representative government and therefore aligns with the harmonizing force; Piggy's glasses represent the intellect's potential to harness the elements and either enlighten or repress). 

Obviously, this is just one interpretation of a novel that lends itself to many valid readings.

Lord of the Flies can also be viewed as a political allegory.  At the end of World War II, one could say there was the "free world" and the Soviet Union.  These two groups can be demonstrated by the two leaders, Ralph and Jack.  The two boys also represent different kinds of leaders and could represent varying political parties. The behavior of the boys on the island could prove as a warning to world leaders what could happen after an atomic bomb is dropped.  Lastly, the "cliques" on the island could represent various social classes (i.e.  Littluns = common folk/everyday people; older boys = ruling class).

The Lord of the Flies is also a biblical allegory.  The boys are literally handed a paradise--warm weather, a beautiful lagoon, no nagging adults, plenty of fruit and berries, and wild game for hunting--a Garden of Eden, if you will.   But because of their own imperfections and inability to control their savagery, they lose their paradise.  They do not listen to Christ-figure Simon, who tries to warn them about their destructiveness.  Instead, they murder Simon and later set fire to their paradise and come very close to destroying not only the island but themselves as well.

The Lord of the Flies is also a biblical allegory.  The boys are literally handed a paradise--warm weather, a beautiful lagoon, no nagging adults, plenty of fruit and berries, and wild game for hunting--a Garden of Eden, if you will.   But because of their own imperfections and inability to control their savagery, they lose their paradise.  They do not listen to Christ-figure Simon, who tries to warn them about their destructiveness.  Instead, they murder Simon and later set fire to their paradise and come very close to destroying not only the island but themselves as well.

The name “Beelzebub” can be traced back to the Old Testament. In
II Kings 1:2-16 (King James Version), the god of the Philistine city of
Ekron is given the name “Baal-zebub,” meaning “Lord of Flies” in Hebrew.
In post-Biblical Hebrew, the name became transformed to
“Beelzebul,” which can be construed as “Lord of Dung” (Gaster 374).
This connotation, along with the name’s etymological association with
flies, probably accounts for the fact that in certain Jewish religious texts
the fly is considered an impure creature symbolic of corruption and evil.
The Berakhot of the Talmud, for example, states, “The evil spirit lies
like a fly at the door of the human heart.”

This somewhat lengthy quote is taken from a commentary on "In the Lake of the Woods" (Tim O'Brien).  It provides a good link between the two books.  In Lake, the flies are evil/Satan, always there during the Mai Lai experience in Vietnam; they are the presence of Satan.  In "The Lord of the Flies" we see Satan himself at work in the hearts of what we might have thought to be the "innocents."  Much like snakes, flies always seem to have some kind of "uncomfortable" if not outwardly evil about them; perhaps the fly's attraction to garbage, and it's unwillingness to leave us alone despite our best efforts makes it a great reminder of our tendency toward evil.

You might want to read the entire article referenced below.

The island itself is an allegory for society. The author shows that, like children stranded on a deserted island, society can break down due to bad leadership, mob mentality, and a lack of true civilization.

James Stern of the New York Times said that the Lord of the Flies is:

an allegory on human society today, the novel’s primary implication being that what we have come to call civilization is, at best, not more than skin-deep

An allegory is an extended metaphor in which characters and/or symbols refer to abstract things, stories, or real aspects of human life. For instance, Ralph is an allegory for a real life democratic ruler who is ineffective because the community devolves. Jack is an allegory of the typical dictator who rules by fear and intimidation. 

Golding used R. M. Ballantyne's 1857 novel The Coral Island as a basis for this story. In Ballantyne's book, some boys are stranded on an island and the only threat is external: cannibals. But in Golding's novel, the threat is internal: the boys themselves. Unlike Ballantyne's group of civilized boys who remain reasonable, Golding shows that these so called civilized, British boys are capable of devolving into savages. He calls attention to the fact that even civilized people can resort to barbarism and violence. So, whereas the British boys in Coral Island only feared the cannibals, the boys in Lord of the Flies have only to fear themselves. This is an allegory of the state of the world following World War II. With the ongoing threat of nuclear war, there is always the danger of such a thing occurring. In this case, Golding's novel is a political allegory of the world following World War II. This is a world that proved its capability for violence in that war and the subsequent Cold War keeps the threat of violence alive. 

It it also a psychological allegory in Freudian analysis. Jack is the "Id," that which is responsible for desires, impulses, and seeking gratification regardless of ethics or human sensibility. Piggy is the Superego, the censor of the Id. The superego monitors the Id and tries to control its impulses. Ralph represents the Ego, that which mediates between the Id and the Superego. 

The novel is also a Biblical allegory. Here we have a group of people placed in a paradise. It is up to them to work together and avoid the temptation to do any evil or go against God's moral and ethical lessons. Like Adam and Eve in the story of the Garden of Eden, the boys (lured by Jack, a devil figure) disobey moral codes of conduct by giving in to baser impulses. 

One interpretation of "The Lord of the Flies" is as an allegory of good vs. evil with the island respresenting a type of Eden.  On this picturesque island of idyllic climate, replete with fruit and meat, Ralph in the opening chapter removes his clothes and bathes in the water as an act of a baptism, accoring to some critics.  This baptism, however, is not sufficient for the removal of sin since the island is a false Eden as there is corruption already within the inhabitants.

The idyllic life of the island is corrupted by the fear of the boys, a fear that they call "the snake thing."  This "snake thing" is not like Satan in the Garden of Eden, though, because it is not external; rather, it is the innate evil impulses that the boys possess.  So, while Ralph represents the golden boy free of sin, Jack, and especially Roger, represent the evil inherent in man, an evil that without the controls of society  dominates.

On the other hand, Simon is the character who is intuitive, spiritual, and much like the prophet who comes to warn of evil. His confrontation with the "beast" who represents the devil is likened to Christ who after 40 days in the wilderness confronts the Devil. After this confrontation, Simon tries to warn the boys, but, like many prophets, he is rejected and even killed by the evil forces of the island.

In the end, the boys are rescued by a savior in the form of the naval officer.  But, he, too, is of innate evil as he is from a war-torn society, so the promise of salvation is certainly marred as suggested by the officer's glance to the warship.

The allegory is of the island.  It's a micro-society representing a small version of the real world.  From the beginning of the book, the reader has to assume that Britain is at war.  The plane was escorting a bunch of boys from their private school out of harm's way.  Then when it was either shot down as some believe, or even something nuclear killed the engines of the plane causing it to go down, the boys formed their own little society.  The themes used in the novel by Golding mirror what society was doing while they were in school.  Civilization is in ruins and the only way to really survive is by savage instincts. 

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. 

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.

Metaphor and allegory, as the answer above indicates, are similar; both of them make comparisons, but the primary difference between them is the depth of the comparison. William Golding's Lord of the Flies is a highly symbolic novel, and he uses both metaphor and allegory to make his point. 

One of the most recognizable metaphors Golding uses in the novel is the beast. While the term beast is used to name many actual things in the story (such as creeping vines, pigs, a parachutist), Simon recognizes the truth that they are the beast. Golding is comparing what the boys have become--out-of-control savages who have no restraints or authority which they must obey--to beasts. In his conversation with the pig's head known as Lord of the Flies, Simon discovers this truth:

“Fancy thinking the Beast was something you could hunt and kill!” said the head. For a moment or two the forest and all the other dimly appreciated places echoed with the parody of laughter. “You knew, didn’t you? I’m part of you? Close, close, close! I’m the reason why it’s no go? Why things are what they are?”

That is the metaphor: the beast is them. 

Golding's use of metaphor on a larger scale becomes an allegory. These proper English schoolboys, who do know how to live in a civilized manner and obey rules, are deposited on an island on which there are no adults. The only rules they have are those they make for themselves, but those are soon ignored or broken. They live without any restraints and they eventually become what Golding calls "savages." They destroy and they kill, things they would never do in their "real" worlds.

What these boys (and remember, they really are just children) do and become over the course of the novel is a picture of unchecked human nature. Their transformation from boy to savage is the allegory Golding uses to make this point.

There are actually quite a few biblical allusions and allegories in Lord of the Flies. Some are more obvious and more developed than others but it is not difficult to spot them.

One of the most developed and interesting is that of Simon as a Christ figure. He is given a number of characteristics including a kindness to the younger boys and an ability to go between groups without prejudice. He also begins to see and understand what is happening when none of the other boys can. He has prophetic visions and actually comes to share his understanding with the boys, but he is eventually killed. This can be interpreted as him dying for their sins and their descent into violence.

Golding suggested that perhaps the two sides of the island represent damnation and salvation. He then goes on through the action and implication of the novel to suggest that mankind will never reach salvation, that they will be stuck on the dark side (Castle Rock) of the island.

One can also look at the relationship between Jack and Ralph as mirroring that of Cain and Abel. Jack gets jealous because the boys like Ralph better and so, in the end, resolves to kill him.

There are other physical references that can be interpreted as allusions as well. The creepers being "snake things" and representing Satan and the dark side of humanity. The island itself can be interpreted as being the Garden of Eden.