LAST POST OF SPOILERS.
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Mid-Boss (officially the name is hyphenated. THE MORE YOU KNOW): Laharl's father (or his spirit. Or reincarnation. The games aren't very clear on this), I think everything he does was an act to watch over or help Laharl. Even that's not entirely clear, as the Wiki states that it's hard to tell what parts were him acting and what was his actual feelings.
Nightmare Moon: Debuted as a villain, turned good by the end of the pilot episodes. Was good in her return appearances in Season 2. More memorable as a villain so I'd include her, but it can be argued.
Q: Was testing humanity as a judge, but often had the species' best interests in mind. Got a lot of nominations and has been on "best villain" lists though, so I seem to be in the minority.
Sue Sylvester: Has had so many episodes dedicated to showing her as a nice person...an antagonist, but probably not a villain in most episodes. Though at times...another of those borderline cases that could go either way.
Tim: Eesh this is a hard one to explain. LOL CRAZY SYMBOLISM. I can't find the explanation I need to link to (as usual), but basically the Princess is symbolically the atomic bomb and the game is a metaphor for the Manhattan Project. ...It makes sense in context. As such, while Tim's actions may not have been right, I'm not sure you could call them villainous without also calling everyone involved with the atomic bomb's creation as also being a villain. It's...difficult to explain and then there are alternate interpretations of the events. Bleh. Probably better off just letting Tim in and ignoring this entire paragraph as this too much of a headache to think about.
Wario: Villain in Super Mario Land 2, then he became a main character and starred in a lot of games where he was just very greedy rather than evil. Often categorized as an anti-hero, I'd say he's more notable for all those occasions as opposed to Land 2. Did debut as a villain though, so it's arguable.
Keep
Angelus: We also saw Angelus on Angel. At one point, Faith goes into Angel's mind (or something like that) and Angel/Angelus argue and fight with one another. Angelus is part of Angel, but a separate personality and if they can have fights with each other I'd count them as being different characters. I admit that it's debatable and won't put up much of a fight if he's removed, but I think they're different enough to count.
Boba Fett: *shrugs*. I count him as a villain, but have nothing to add.
Ghaleon: Best known as being a main villain, didn't do much when he flipped back to the side of good, was evil for the entire time he had the "Magic Emperor" title. Can be argued for removal, and it certainly is worth having the argument, but I'd keep him.
Perona: Seems to have been bad for the majority of her appearances, though I'll admit to not knowing much at all. Suppose those more versed in knowledge about the series should argue about it.
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SPOILERS BE ENDED
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In this world which will someday fall to ruin...
...dreams and hopes don't matter at all.