Frieza's definitely Top 3. Still maintain that the series should've ended after he was defeated.
Never read Monster in full so I can't comment on Johann.
Sensui is cool, but he was easy to sympathize with. Best villains to me just don't give a fukk because they don't see a reason to. Unsympathetic, unaffected, just handle business.
I saw someone post Griffith/Femto but it's not fair to say that until Berserk ends...if it ever does.
Bradley/Wrath from FMA...
Saw someone mention Shishio. Great fukkin character, but his motives were actually somewhat honorable in a nationalistic sense, even if he was extremely brutal and borderline tyrannic.