I can defend Hiroshima and Nagasaki as military targets. I actually have a greater trouble defending the firebombing of Tokyo (though, its pretty clear to me that the capitol of a combatant country is probably a valid target for bombing in a declared war) because of the sheer number of casualties.

One of my gripes about WWII in the Pacific Theatre, is some folks get very bothered by use of nuclear weapons, while ignoring or downplaying the use of incendiaries, which often killed far more people.