It's entirely dependent on what it is you're doing. If killing one innocent man would save 100, it's reasonable to say that's justified. But if killing one innocent man would only save 2, well that's a lot more debatable now isn't it?
The kind of situations in which "The ends justify the means." apply, should only ever be taken on a case-by-case basis. And not just the means either. The ends are also something to think about. What if "the ends" are only good from a certain point of view? I bet there's PETA members out there who would like to systematically steal every pet from its human household and set it loose on the streets. But not only do I disagree with those means, I also disagree with those ends because that means stray dogs and cats everywhere, running out in front of my car and knocking over garbage cans and biting at my legs.
I mean no offense to those of you who voted "Yes" or "No". But you were all probably thinking of some kind of isolated incident, or maybe thinking of the general context in which "The ends justify the means." is usually used. There's a good example of this in Modern Warfare 2, on the mission "No Russian", in which you play as an American marine sent to HELP a small group of people commit a serious act of terrorism. You are asked to assist in massacring hundreds of people at an airport, to get in good with the leader so you can sabotage and capture him later. And this mission is morally debatable. I imagine most of us would probably be against something like that. I don't agree with it at all. But there IS a legitimate argument to be made in favor of it. And it does beg the question, "Do the ends justify the means?" I get the feeling a situation such as this one is generally the kind that people have in mind when they hear that phrase.