Bloody hell this is a tough one... Now I have several different favourite villains for several different reasons... ( Just so you know I made this SOOOOOO much harder for @Glen-i )
I've deliberated on this for a little and as much as this was a difficult choice I've decided on...
The Ashford twins ( from resident evil code Veronica )
In particular I am talking more so about Alfred Ashford!
Two twins separated from a young age based on their intellectual differences, Alfred left to idolise his sister, though being of higher then average intellect, his sister was a genius. Alexia given the priority of the two graduated from university at the age of ten. They both were moved to the Antarctic base where Alexia conducted her tests on the T-virus.
The two children discovered the truth about their origins after gaining access to Alexander's lab. Disgusted by this fact, the two forced him to take part in a human trial of t-Veronica, and then left him sealed in a hidden compartment beneath the facility director's office. Soon after, Alexia found out how to properly control the viral corruption, but the process involved fifteen years in cryostasis. Alexia left this task to Alfred, and with no choice Alfred aided Alexia in her Complete mad dream of Godhood.
Alone, in the world Alfred's mental state shattered and with that a dual personality developed within him closely resembling that of his sister. His mental state eroding so far as to dress and having conversations between each dual personality.
In there is a tragic irony... We learn of Alfred's tragic mental erosion and at the brink of death he makes his way to the cryogenic pod where Alexia is stored. And finally the twins are reunited, though Alfred passes away as Alexia strokes Alfred's head as he lays dead in her lap. Leading to one cut scene that still gives me goosebumps to this day.
( Warning, tasteful nudes ahead! )
Oh... And this is an extra little clip because Alfred's voice is just amazing and it makes me smile every time.