Taking "allegory" in the sense of "an act of interpretation," herewith a few possibles readings:
Ralph: the individual in society; this is suggested by the point of view which tends toward limited omniscient through Ralph's perspective. In this reading, Ralph represents each one of us attempting to lead our lives as each of the forces described below exert its influence
Jack: the animalistic, or (if you're an animal lover), the pre-rational (for our purposes the non-rational) impulse in human beings to satisy our physical, material desires without regard to the consequences; unchecked, this inevitably leads to violence and cruelty
Piggy: the intellectual or rational faculty in human beings, which, if not tempered by the other forces within us, becomes selfish and vulnerable to the non-rational force
Simon: the emotional capacity in human beings which is moved to serve others; while extremely potent, when it comes into conflict with the 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.