Generally speaking, my PCs have killed monsters / NPCs because...
... they were iredeemably evil (undead, demons, devils, etc.)
... they attacked us first
... they attacked NPCs the PCs were obliged to protect, or who other NPCs engaged the PC's services to protect
... they were at war with the PC's country
Ding - ding - ding. Pretty much all that applies in the current adventure (sorry, over email, so no last "session") in my campaign.
The PC's were tracking and found a group of werewolves (in my campaign and in 3.5 RAW, ALWAYS Chaotic Evil).
The werewolves are a mix of orcs, half-orcs, and human barbarians. Together, they are a band of mercenaries serving a foreign country, and they came to the PC's country on essentially a terrorist mission -- attack a small village and kill everyone, to draw back troops from the frontlines.
The PC's were sent to area by the central government, because the local baronet wouldn't send his troops to the front when ordered to, claiming trouble with orcs and wolves. The PC's (5th-7th level) scoffed at such puny issues and vowed to clear it up quickly and shoo the Warriors to the front.
The next night of the full moon, the werewolves attacked and burned a village. The local militia forces managed to cover the civilians escape and kill a lot of orcs, with some losses of their own, until the one mounted PC and some mounted NPC allies arrived and drove off the werewolves. (All done round by round, since it's email you can do a lot of NPC action in little game time.)
The second time, the werewolves tried to storm the baronet's tower (where the civilians were sheltering), thinking they were just fighting the one PC and militia again. They split up their forces to try and get the baronet and bite him, but they got pwned as the baronet succeeded at bull rushing his attacker out a window, and the PC's blasted a lot of spell power and some elvish archery at them. The PC's killed one and captured (and turned over to the local lord) two of the leaders.
With a sergeant from the local lord's militia, they've been tracking the last remnants of the mercenary force, and just found them. Their mission is to kill or capture them all, to prevent spread of the plague of lycanthropy and to find out where they came from and how they slipped into the country. Which lead to big, knock down, drag out fight.
They take prisoners because they want info on who the attackers are and how they got here, and because it seems to be the good thing to do to them. As DM, I'll likely have the werewolf prisoners hanged for brigandage by the local authorities, but I might do something more interesting like an escape or a prisoner exchange, who knows?