For me, probably a tie between Scarpia and The Queen of the Night. I would say that Scarpia has a cooler part, but I like the fact that the Queen of the Night being a villain comes as a bit of a twist. I don't really know a lot of the repertoire though. I'm trying to go through the operas I know, and I can't find too many villains. A lot of operas have antagonists or nasty characters, but it's hard to call them villains, since the motivations are generally much more subtle than just being evil or malevolent.
For example, here's a little analysis on the possible villainous characters in Der Ring des Nibelungen.
Alberich is obviously in villain territory, but I don't think Wagner paints him as a totally unsympathetic character. He legitimately gets screwed in Rheingold, and tries the rest of the cycle to get his property back. Is that so bad? I guess it wouldn't have been good for nascent humanity if Alberich became an all powerful lord like Sauron or one of those bad guys in Lord of the Rings, but is he much worse than Wotan and company? Other bad characters in Der Ring include Hunding, Fafner, Mime, Hagen, and Gunther.
Yeah, Hunding is really bad, though as he says, it was his people's tradition to do what he did. In ancient times, kidnapping wives was probably fairly common. (Sadly, it's still probably common in some places even today).
Fafner isn't so much a villain as an obstacle, since all he does is really sit between Siegfried and the ring. You can't totally blame him for his actions since the real reason he killed his brother was because of Alberich's curse.
Mime is, of course, a nasty character, but you also have to feel bad for him since he got terribly bullied by both Alberich and Siegfried.
Hagen- I guess I would say he's the most purely villainous character in Der Ring. He has a bit of an excuse given that he's acting on Alberich's behalf, but since he actually stabs Siegfried in the back, he gets most of the blame.
Gunther- hey, he's just desparate for a wife. (and Hagen talked him into it)
I think the "villains" in some other operas have similarly nuanced portrayals and motivations. Though, of course, there are some real bad guys in operas as well.