Damn this is a hard one :3 They're all so badass, probably my favorite set of villains in Sailor Moon. I pretty much like 'em all except for Mimete, Cyprine+Petitol, and Master Pharaoh 90... Mimete was funny and cute, but kind of annoying; Cyprine+Petitol were introduced too late and had too little screentime to have much of anything interesting about them; and Master Pharaoh 90 had nothing but backstory.
I guess Professor Tomoe, Mistress Nine, and Kaolinite are my favorites. Professor Tomoe was funny but also sympathetic, Mistress Nine was badass, and Kaolinite was creepy and hot. Eudial was cool, too; funny but also sort of badass, managed to do a lot before her death. Viluy and Telulu are also pretty cool and I like their designs a lot, wish they could've gotten a little more screentime tho. I could've done with less Mimete, and a little more Viluy + Telulu.
By the way, I'm mostly going by the 90's anime in regards to this; I'd say in the manga/Crystal, I'm more neutral to all of them. If I had to go with a favorite from the manga/Crystal, it'd probably be Mistress Nine or Kaolinite. I like Professor Tomoe a lot less in the manga/Crystal, I didn't like how he was pretty much all evil without a more human/third-dimensional side.