If it's crap ... We'll tell you
It doesn't happen a hell of alot with me, but there are times where I actually sympathize or support the antagonist I'm supposed to fight against or even hate in a video game. For example, I couldn't really hate Hugh Darrow for what he did at the end of Deus Ex: HR. Granted I sure as hell didn't agree with him, but I understood his frustrations and why he went in the direction he did.
What about you all?
Felt pretty bad about killing Sniper Wolf in MGS.
And though "villain" may not be an apt term, you can bet your ass I sympathized with The Boss in MGS3.
I'm sure there are better, non-MGS examples, but those are what currently come to mind.
I always kinda liked John Henry Eden from fallout 3, sure he was a computer who thought he could be a better president then a human but he was voiced by Malcolm Mcdowell so I was suckered it.
The Boss, given that a lot of people are going to mention her on this thread I'll go for a more unique answer:
Just remembered - Godot from Phoenix Wright. Hell, I still to this day have trouble even thinking of him as a villain at all.
Caius from FF 13-2
Yeah, Illidan really got the raw end of the deal in Warcraft 3 and The Frozen Throne. I'm not really sure about anything in WoW, though.
Second. First one that came to mind when I saw this post.
She isn´t realy a villain i think but i felt bad after killing priscilla from dark souls.
She just stands there at the end of the painted world and even tells how to get out doing no harm to anyone, killing her made me feel like a huge dick.
Agreed. I would also add the Moonlight Butterfly and Sif to the list of Dark Souls bosses that triggered a bout of post-battle depression.
Perhaps I haven't been playing the right games, but I can't recall many villains I've sympathized with on an intellectual level. I have sympathized with villains in a more visceral sense; Alessa from the original Silent Hill is one noteworthy example (though it's debatable whether or not she can be considered a "villain").
In Parasite Eve (*14-year-old-game SPOILER ALERT*), I remember being taken aback by Aya's comment to the Ultimate Being right before the final showdown: basically, she acknowledged that it had just been born and is merely trying to stay alive, but it poses too great of a threat to mankind to live. The game ditched the monochromatic "black and white" pretense so common in video games and instead chose to highlight an existential conundrum in the very nature of conflict: That two opposing entities both wish to survive, and the victory of one means the death of another. While, at first glance, this may seem stupidly obvious, it brings one striking implication to the table: That you and your enemy are, on some level, the same. Suddenly, it's not a case of righteous good versus faceless evil; it's a compromise. That kind of depth in a video game story is a breath of fresh air, particularly when action games have a propensity for one-dimensional villains that merely act as obstacles rather than sentient entities.
To be fair, though, that can probably be attributed to the fact that the game was based on a novel, as Square doesn't exactly have a strong history of creating deep, nuanced characters in their original IP's.
(*End spoiler alert*)