Nah, those are the most annoying, LOL. In any form of media, any time I come across a villian who "Is doing it for the good of his country" or whatever, I just want to either puke, or jump into the book/movie/game/whatever and STRANGLE HIM!!!!!!. Seriously, I just can't stand that kind of villian.
Guess you didn't really like Morrowind's villain, then.
Dagoth Ur was allowing the blight and corprus to spread for the good of the Dunmer people, so that he could take Akhulukan and drive the Imperial invaders from Morrowind, when that pesky Nerevarine came and ruined his plans.
I really dislike villains that are evil-for-evil's-sake. It's so 1-dimensional, flat, and boring. Even Oblivion's main villain (Mankar Camoran) felt he was doing "good".. he was trying to reclaim the imortality and godhood that elvish beliefs say were wrongfully stripped from them by the trickster god Lorkhan with the creation of Mundus. In contrast, Mannimarco really fell flat by not having an in-game reason for attacking the Mages Guild.. he was just being evil because he wanted to be evil, so I never cared about his goals..I just needed to kill him to finish the guild quests. Bethesda really should have played up the "necromancers are being unfairly banished and are retaliating under a new leader, Mannimarco, who's himself fighting an centuries-old grudge against the Guild because of disagreements with its founder" angle, but instead it devolved into "we kicked evil necromancers out, and they're rallying under Mannimarco, and he's like, evil and stuff, and you need to kill him because he's, like, evil. He gets into our base and kills our dudes."
I like antagonists (villain is really the wrong word, here) that think they're doing good, or at least have a very good reason for what they're doing. There's two sides to every conflict. I'd like them to have a reason good enough to make some player characters possibly believe they're right, and join them. But if you're going to go that far, don't wimp out and disallow players from joining the other side.