King Bob-omb (I love his voice acting and is big mustache.)
King Boo (Never really played any Luigi's Mansion games but I like him all the same.)
King Thwomp (We build your houses, your castles, we pave your roads, and still you walk all over us.)
Small/Big Cosmic Clone (Specifically the one from 3D land. Is he a creation of Bowser Jr. or some other force out to get Mario?)
Il Pianissimo (I wouldn't really call him a villain, but still, why does he wear a mask? What's he hiding? And that scene at the end of the game, very suspicious if you ask me.)
It's hard to place these guys in any particular order. But King Bob-omb is number 1 for me.