I think the type of discussion this thread brings up brings two gamer ideals in direct conflict with each other. One gamer ideal is that we want our games (at least some of them) to become deeper and give the player a sense of purpose the things they do while they play the game. They want a better reason to play a game besides scoring another point and beating a level.
The other gamer ideal is that ultimately the ultraviolence in video games doesn't matter and there fore can not be ethically wrong. When you kill some one in a video game, they are often shallow and flat, and are cartoonish exaggerations of real life people, giving the player no moral dilemma at taking their life. If the player has any empathy toward the people they are killing, then that immediately detracts from the fun of the game for them. Very few games actually let the player realize just how terrible their actions would be if they were actually hurting real people. The best example of this is Grand theft auto. Besides the NPCs that you receive your missions from, every other character in the game is selfish, rude, and stupid. At the begining of the game you might have some moral quandary about driving on the side walk, but once you hear how the people talk about you behind your back, you realize that they are not human.
I'm sure there is more than one game that has made me feel bad about killing an enemy, but the one that comes to mind the most is Bioshock. I remember one time that I found a way into a locked room and there was a splicer sitting on the couch, crying her eyes out. I knocked the grate out of the way, and then she looked up from her hands and said something like "Whuh?". I didn't even change back to my gun to kill her. To me, she had just become another victim of Rapture, a woman hiding out in a locked room. But then she suddenly screamed in rage and in a panic I pulled the trigger and she fell to the ground dead. I remember searching the room frantically, trying to find an audio diary to know more about the person I just killed, but all I found was some standard loot. I will probably remember that woman for the rest of my life, but according to that game she was just another enemy.