I'm looking for superhero books like Avenger's Civil War and the Justice League Unlimited cartoon where there is a dilemma and cold war going between independent and government loyal superheroes.

Superheroes traditionally are vigilantes who take justice into their own hands. On the one hand this approach can be more effective at savings lives and doing good if the proper channels are inefficient, slow and full of corruption but on the other hand this is a dangerous precedent as one person's idea of justice may not be objectively just and could inadvertently cause chaos.