Alright, I'll start off.
Dio Brando (JoJo's Bizarre Adventure): Now, at first I despised Dio. He's probably the biggest dickface I've ever seen in any series. But, by the tiem I reached him in Part III I saw how much of a well developed and badass villain he was. He's probably one of the most well developed and charismatic villains I've ever seen, not to mention his stand, "The World," was my favorite in Part III. He's just a total badass… even though he still pissed me off (I was furious when he sucked Joseph's blood). You know you have a great villain when you can despise him and admire him at the same time.
Yoshikage Kira (JoJo part IV): i didn't really like Kira as much as i did his background. I like his background a lot because it is a lot like the typical serial killer; an average, introverted, yet brilliant neurotic who didn't want to stand out. I like it when I'm able to tell when an author did their research. Plus, Killer Queen was a pretty sweet stand (Well, except for Bites the Dust. That was a bullshit power.)
Piccolo (Dragonball; both Ma and Jr.): Just a classic awesome villain. Them ore I think about it, the more Piccolo is my favorite DBZ protagonist. It's a shame he was pushed aside by Vegeta and the other new Saiyan characters, though..
Buggy the Clown: Just...awesome...
That's all I can think of for now.