There is a strong argument against the officers of the Wehrmacht and Waffen-SS at the post-World War II Nuremburg Trials in which those who issued orders that led to the killing of about 12 million civilians. The main argument for defense, as themusic mentions in hir writeup and the node title subtly gives away, was "I was only following orders."
For those like Adolf Eichmann or Josef Mengele, that response is hardly viable. The Nuremburg trials convicted many officers, generals and SS-Obergruppenführers who used orders as an excuse for their conduct in the war. These men issued orders and carried out their own inhumane actions without prompting from a higher echelon.
However, I believe one should draw a line of distinction between those who had the power to issue orders and those who had to carry them out. There were generals who did their best to counteract orders from above that were against principles of humanity; General der Flieger Alexander Andrae comes to mind. Generals and high ranking SS officers had the ability to resist or water down orders (even if just some) that were immoral. However, enlisted boys usually did not.
Place yourself in the boots of a citizen in Germany, 1940. You had no choice in the National Socialist party coming to power, you had no choice to be born in Germany and because of restrictions, you cannot escape to a neutral country such as Switzerland. You are required to join the Wehrmacht as every male of your age group is. Your conscience tells you that the Nazi party's discrimination of various groups is wrong, but you are going to be in the Werhmacht, far away from the atrocities of the death camps. You figure you are probably bound for battlefields of France or Russia or perhaps the Battle of Britain. You think you will not face any dilemma with Jews or gypsies or whomever. Until one day you are given a notice, you were conscripted into the Waffen-SS, along with another 200,000 Wehrmacht guys, to be sent as guards to a concentration camp. You are to be supervising the inmates' work on aircraft. You are under strict orders by the kommandant to shoot any prisoner who tries to escape, and conversely the kommandant is under strict orders to the same effect by Heinrich Himmler. Now you are an unwilling guard at a concentration camp who could risk punishment if you fail to "execute" your duties in shooting an escaping prisoner. That punishment could mean reassignment to a penal unit in Dachau and perhaps a death sentence, even.
Your conscience tells you that you shouldn't be working these facilities for the Third Reich - it's immoral! You can't shoot an unarmed civilian, that goes against your principles. But these men with guns and authority tell you to do so, and if you oppose orders of an officer, you risk death even yourself!
This was not the case with all of the guards in concentration camps, but it was the situation for many. Yes, there were ruthless killers among them that thrived on the opportunity provided them by the government. Everybody is not the storybook hero who can stand up to a whole governmental system and a whole military, as a young recruit, on moral grounds. Now, are these boys war criminals or are they too a sort of victim of the Nazi system?
It is very easy to cast those such as Heinrich Himmler and Josef Mengele as war criminals that deserve to be hung, but can you say the same for those that truly were just following orders and those who had no say in the matter? Can you convict those who follows orders for the sake of their own life? Roman Catholic Church doctrine says that to the extent that one's free will is limited, one's responsibility for those actions is just as limited.
This model of limited responsibility with limited will can apply to any situation with military orders and even beyond the scope of the military. I've used the example of the defense used at the Nuremberg war tribunal after World War II because this defense is mostly known through those trials and their defendants. This example also presents a good model for a government or military forcing its citizens or members to perform immoral acts.
My point in this is that all those involved in the concentration camps of Nazi Germany were not war criminals, benign or otherwise, but were simply boys forced into cooperation with the Nazi war machine. Therefore, do not automatically issue a mental guilty conviction to a person whose defense is "I was only following orders". Consider their situation and the extent of their free will, first.
Reference for conscription information:
http://www.wssob.com/000ttwsb.html (Insignia section)