"Depending on the method used to kill an important enemy like Orthag, you get a rune tied to one of those weapons. Since Orthag was killed in open combat, Talion receives a rune for the sword that boosts melee damage, but at the cost of a lowered regeneration rate. Several of these runes can be slotted in each weapon, and the more powerful the enemy, the greater the rune. That's why it might be in a player's best interest to sometimes allow enemies to escape and gain power and prestige; their eventual rune reward becomes all the sweeter."
I took that from the GI article. Lots of games have asked the player to choose life or death for an innocent or even morally ambiguous NPC but about the only time a true villain escapes is during a scripted sequence that advances the plot. Has anybody ever played a game where you actually contemplated it being a GOOD idea to let your arch enemy go instead of killing him on the spot?