As far as animes go, I would like to nominate Lloyd Asplund from Code Geass: Lelouch of the Rebellion.
For those of you who've seen the anime but don't remember him,, he is the guy with the white hair and glasses who is part of the R&D section of the Britannian military, and is also the brains behind the advanced Knightmare Frame Z-01 Lancelot (the white KNF that Suzaku pilots.)
Although it's never mentioned directly in the anime, there are some very obvious clues pointing to him Asperger's Syndrome. For one thing, one of the running jokes in the anime involving him is whenever he says something weird or rude, his assistant Cecile always offers him "a lesson in proper social ettiquite", to which he responds "no thanks, I'll pass." Also, he ends up being engaged to Milly Ashford, a schoolgirl friend of the protagonist (it's an arranged marriage), but the few times that they are together, Lloyd prefers to rant on about scientific crap rather than attempt to be sociable. During one scene he goes off on a detailed history of a obsolete Knightmare being used at a festival at Milly's school, after which Cecile remarks to her, "So now you know. He really has no interest in the opposite sex."
Yeah, he's a character all right:
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