Alas, poor Meepo, I murdered him well.
One of my first, if not my first, Dungeons and Dragons 3rd Edition campaigns (in which I was a player) was a module. I was playing a lusty spearman, rash and ready to fight. The first monster we encountered was a lone kobold, shivering beneath a blanket at the entrance to some caves, or perhaps it was a ruin of some sort, I don't recall which. Spoiling for combat, I speared the poor creature, and threw him over my shoulder like a farmer pitching hay.
The first half of the dungeon was more of this. Room after room of kobolds felt the taste of my spear, until we finally encountered the shamanic leader of the creatures. She just happened to speak common and informed us that these particular kobolds were peaceful, but had been fighting a war with the goblins who occupied the ruins farther in.
She also gave us the name of that first kobold, who I unceremoniously annihilated, Meepo. Meepo also spoke common, and had I not snuffed him with extreme prejudice, would have informed us of the plight of his people, and pleaded for our help against the goblin horde.
Stricken with guilt, I swore to the kobold leader that I would set right the wrongs I had perpetrated. As our party had decimated the kobold's forces, we vowed that we would expunge the goblins from their midst.
So we killed them all. Every goblin. The men, the women, and children. Some were slaughtered in their beds. When we came upon the goblin warrens, I found it easier to just set the whole place ablaze rather than have to go searching through its myriad of tunnels.
Our vow fulfilled, we left. On that day, my lawful good warrior learned three lessons. Two wrongs do not make a right, honor is a harsh mistress, and, if possible, speak to your enemy before you shove your spear through his chest. Still, my warrior carried the guilt of his actions for the rest of his days.
Almost every adventure should leave scars on your characters, most physical, some mental. Talk to a veteran of any war and they'll tell you about the pride and glory of combat, but they may also tell you about the horror and insanity of conflict.
Even if your current adventure is not a war, there will likely be bloodshed. And while the leader of the opposing force may be a megalomaniac, odds are, most of his troops are not. Be they bandits, drow, orcs, goblins, or anything else sentient, I believe it is the duty of a good DM to make sure that the players realize that they are not only killing enemies, they are also killing husbands, sons, daughters, fathers, and mothers.
There always two sides to every story. Too often in RPG's are we only presented with the heroes tale and never stop to ponder the fate of his enemies.