Boogiepop is called a villain, though he/she never came off as one to me. In Perfect Blue, MiMania and Rumi along with Mima herself are all really good female villains.
In Gatekeepers 21, Tomokazu was rather dashing even if he wasn't a villain. Legato...Viscious.... Ajo from Key: the Metal Idol wasn't cute, but he made for a pretty good villain, though I liked her voice teacher more.
I have a couple...
The Kisenian flower from Sailor MoonR Movie
The Professor, Mistress 9, and the Witches5 from Sailor Moon Super
Queen Nehelenia from Sailor Moon SuperS and Stars
Sailor Galaxia and her Sailor Anima-mates
Soi and Nakago from Fushigi Yuugi
Pyoko from DiGiCharat
Mikage (the fisherman) from Ayashi no Ceres
Rumi from Perfect Blue
Morigan from Vampire Savior
Heh, I have seen so many anime and it's hard for me to think up some actual villains... There's always an antagonist, but many don't qualify as true villains in my opinion.