The greatest villains ever written are ones fans hate but can't help sympathize with. A foe with no reedeming qualities or understandable motivations would simply be cartoonish to most gamers. While there are still some games that make use of a one-dimensional and inexplicable evil enemy, there are games that showcases villains that show quite some depth even if we do not see it so easily.
Here are some of the villains that I think are misunderstood by most gamers. If you look closer, these characters have motivations that we can sympathize with and perhaps they were simply misguided along the way. I'm not justifying their actions, but showing that sometimes these villains can be victims of trauma and ambition.