One huge problem with spec-ops missions is that there is often no plan for taking prisoners. If you arrive on the scene via a rope from a helicopter and you're planning on leaving in some other "lightweight" way, you can't very well take prisoners. And you can't leave them because even if they surrender to you, if you don't actually arrest them they will become a threat as soon as you leave. So we're sort of back to a defensive posture: kill-or-be-killed. This is what got Senator John Kerry in trouble for, I think -- Doug Velentine's take on this ("War Crimes As Policy") notwithstanding.
I think these kinds of operations are getting better: in Somalia (before The Plan went horribly wrong), they were prepared to take prisoners: although the Rangers roped in, they were going to drive out in trucks. Many non-lethal weapons are able to be employed in these kinds of missions now (even something as simple as plasti-cuffs means you don't have take someone with you and you don't have to kill them either). Nevermind that it didn't go that way ...
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I wanted to clarify that Matt was looking for an a priori distinction between "act of war" and "crime" in the case of the attack on the WTC. I think it's clear that the workers in the WTC were neither armed combatants (even if you believe that it was an act of war, which I don't) nor "merely" collateral damage: they were the primary target.
That's what makes it a crime.
/jordan