This could be a difficult topic to judge. For example, I can think of terrible villains who did terrible horrible things, but honestly, someone else is responsible for it.
Take Luca Blight from Suikoden 2. Now, Luca attacked the Youth Brigade of his own nation with his personal guard, completely wiping them out. He blamed this on the City-State to put a stop to the peace between the nations. He then proceeded to burn villages down, mock people as he killed them, and even sacrificed an entire city to awaken a great power. Even managed to kill his father with poison. In one scene, we witness a woman beg to be spared, saying she'll do anything. He tells her to act like a pig, which she does. When she thinks that she maybe spared, he then cuts her down with even more slashes than he did other victims we saw he slaughter.
Terrible villain, right?
Okay, but when he was a child, his family was attacked by bandits. His father got away, but not him or his mother. He witnessed these men rape his mother repeatedly for days. Eventually, they were saved, by the royal guard, but a little later his mother died giving birth to a daughter, most likely conceived during that time. Later, he learns that the men were hired by the leader of the City-State.
Also worth noting, that his father was a good man. The only reason for any conflict was the City-State tried to invade. If you look into the background information, you'll realize that the entire conflict that predated the game, and Luca's worldview is all the result of the former leader of the City-State.
So who is the real villain? Luca is more of a victim lashing out at those who wronged him. Yes, he is a villain by his actions, but can you really blame him? Oh, and he seems to have nothing but love for his little sister. Though, he does ignore her pleas to stop the war. Think about that, for a moment.
Other than that, Seifer, from Final Fantasy 8, springs to mind. Yes, you fought him repeatedly, and he was a dick, but he was only trying to live his dream. It seems Ultimecia was using this to manipulate him. And as we saw, there seemed to be no real hard feelings between anyone and him. You could even argue, if you go with the Squall is Dead theory, that we never see Seifer do anything actually wrong. And don't forget he ran off, on his own, to help Rinoa and attacked the President of Galbadia by himself.
Garland, from Final Fantasy 9, was really only trying to aide his own people.
Light from Death Note. You can easily argue that he was a villain, but how many of you would do different, or even worse things, with such a power? At first, he was really only killing the worst of the worst. He became a little twisted and arrogant by the absolute power that he began to wield, but that's about it.