In my mind its when soldiers stop fighting with the sole aim of protecting the unarmed that acts of war become murder. If people are trying to attack you with guns, you have a right to fire back, unless you started it without it being a matter of saving lives, in which case you are the monsters! But actions like bombing civilian areas with the full knowledge that civilians might be there, even if the enemy are armed and in the area, is murder. There is no excuse for killing civilians, deliberately or as a consequence of defeating the enemy, because it goes against the entire point of having a military, which was originally to protect the nation and now should, in the modern globalised world, be used for peace-keeping and protection of the human rights of people everywhere. Of course, you could argue that a military was designed to protect YOUR nation and still be used solely for that role, but in my mind, thats just nationalist drivel. You'll protect a Briton with your life, but neglect to do so because the person happens to be Iraqi or Afghan? Piss-poor argument for the kind of shelling that the NATO forces (Note that I said NATO and not American, the Americans are not the only nation involved in Afghanistan.) get up to these days. The way I see it, nations are basically administrative areas. We know now (after centuries of nationalist, religious, ideological and racist conflict) that humans are fundamentally the same wherever they are and that it is a matter of background and education that makes the differences (aside from the occasional nutjob) so my attitude is that arms should only be used to protect the unarmed, all unarmed. Wherever they are. What a pity this ideal is a far cry from what actually happens.
To paraphrase Carth of KOTOR: "We're not warriors. We're soldiers. Warriors attack and steal. Soldiers exist to protect people, usually from the warriors." Warriors are whoever tries to use force to abuse the fundamental rights of people to get on with their lives without harassment. Soldiers should protect from those people. (That was a rather crappy attempt to simplify my argument with symbolism.)
On a civilian note, equally, anyone who is trying to attack a non-combatant becomes an aggressor. In my mind, these people are as legitimate a target as an armed soldier whose orders include yours or someone elses death. So yes, the mugger with a knife who is trying to stab that homeless guy for the few coins in his begging cup should be as legitimate a target as a hostile on the battlefield. As long as that knife is in his hand and that hostile intent is there, he should be fair game. After all, in the ever-childish but sometimes valid argument, he started it. (And yes, I've heard stories of people stabbing homeless people for their money, and in some particularly sick cases, for no reason whatsoever.)
Of course, things get complicated in insurgencies, where a warrior may be a civilian five minutes later. It is not unheard of for IRA and Iraqi militants to shoot a peace-keeping soldier dead and then run off, throw away/hide their rifle, and come out in changed attire claiming to have never been in battle. The temptation to crack in these situations must be immense, but to keep the moral high ground soldiers must keep the rule that you only shoot the enemy with a weapon in their hand. Anything else, and your enemy can simply turn around and say "you're no better than we are."
Its also complicated by the "Them and Us" nature of human conflict. Both sides will feel they were the ones in the right. Who decides? I guess this is why we need a UN that is unbiased and works, so there is an authority on these matters bound only by the geneva convention and the charter of human rights. We have solid rules on military force, it is a matter of getting the world to adopt and enforce them.
I'm overcomplicating. To put it simply, killing an unarmed man is murder. Killing an armed man who means no harm is murder. The only justifiable case of killing is if someone is trying to kill you or someone else, and you kill him first. I apologise for the wall of text.