The Emperor, or are we just talking about Earth-Bound fiction? Then technically, Apocalypse from X-Men was born a human, but he's far from human now so I'll just say Harry Potter cos there's far too many to think it throughright now.
I'm going to agree with Nephthys and say that Simon has it or is at least in the Top 5.
Though that Haruhi person has an impressive background from what I saw in her wiki page. Though being described as a crack in the space-time continuun does make her human origin iffy.
__________________ "Compounding these trickster aspects, the Joker ethos is verbally explicated as such by his psychiatrist, who describes his madness as "super-sanity." Where "sanity" previously suggested acquiescence with cultural codes, the addition of "super" implies that this common "sanity" has been replaced by a superior form, in which perception and processing are completely ungoverned and unconstrained"