I think Vincent in
Crossroads; A Johto Story is a good villain. Angsty, tragic backstory, family problems, easy to hate etc.
Heeeeeey. He's not supposed to be the
villain. :x
Anyway, on topic.
My favorite RP villain may be one that has not actually debuted yet in any of my projects, being the villain that believes what he/she is doing is the
right thing. It is a fantastic shift that gives the villain a sense of justification to his/her actions, and provides a great deal of depth in my opinion. Primarily in that their psychology is complex, and as my one friend would say "provides conflict in the reader" since part of them would almost want to cheer for the villain.
My favorite one that has debuted has been one of my own villains in Kasumi Kobushi in OP. I am slightly biased because she is just fun to write, but her archetype is that of the "I'm a lot smarter than you" villain. She is always a few steps ahead of the RPers and her elaborate plan was so fun to design. As far as villains played by other GMs, well, honestly none of the RPs I have joined had either clearly defined villains or got far enough to really flesh them out. It's a sad truth.
I personally prefer NPC villains, permitting they are written by an omniscient narrator who can provide some perspective into the mentality of the character. The villain is meant to pose as the antagonist so there is some purpose for them not to be a PC, or anything like that. They can cause some drama in all the wrong ways if I am understanding the question in that respect. Giving the villain some perspective posts and treating him/her like a PC is a great idea and one I intend to utilize in my own RPs.