I'm not certain this is my definitive answer but the new Metal Gear game got me thinking about how awesome the sniper battle with "The End"
from "Metal Gear Solid 3: Snake Eater"
was. Image: http://media.psu.com/media/articles/image/MGS_Boss_The_End.jpg
It perfectly matched the stealth aspect / theme of the game, it was a slow, meticulous fight, which is uncommon for most bosses, and you had 3 different ways of winning it.
You could either snipe him enough times to kill him, sneak past him entirely, or wait a week (real world time) and he'd be dead from natural causes when you loaded your game.