Batman- is George Bush, Dick Cheney, et al. who understand that the old rules won't suffice. They are the necessary paradigm. For example, Batman wiretaps and monitors the entire populaion of Gotham.
The Joker- is the archetypical terrorist within the dialogue of the Right. He doesn't kill in reaction to what was done to him or what anyone did. He just kills.
Commissioner Gordon- is the police, the military, the FBI, the CIA, the protectors who have their own rules and structure they must perforce follow who work in parallel with the new paradigm.
Lucius Fox- is law and order. Law itself. He provides the tools necessary to fight according to the needs of the new paradigm. He vascillates between cooperation, relunctance, and incredulity until he ultimately has to disavow Batman's methods.
Harvey Dent- is every defeatist, every cut-and-run'er, everyone who started out on the right side of the fight before giving in to despair.
Gotham- is our ideals of right and wrong, rule of law, and noble ideas that can't survive against a new type of enemy.