Death Note has L, many people seem to think he has AS tendencies, he is interesting habits to put it lightly, and also has very little social abilities.
I've seen a video of L (the one where he says, "I want to tell you that...I'm L,"), and he's either an Aspie, or some random-acting person.
Might add Azumanga Daioh, Osaka is very spacey and thinks differently to others, Sakaki is very quite and afraid of upseting others and Tomo well she is probably more along the lines of ADHD.
I've taken an Azumanga Daioh test, and I first got Osaka, and then Sakaki. Osaka could have a co-morbid ADD along with her Asperger's, because I'm either hyper-focused, or not focused at all, which is exactly what Osaka is like (I have ADD and Asperger's). Sakaki might be Aspie, too, as she does seem pretty quiet, introverted, and soft-spoken.
I'd also suggest that hikikomori in Rozen Maiden (although I forgot his name) is an Aspie, but maybe he's not. Lain from Serial Experiments Lain seems like a good fit, too.
Niea from NieA seems like she has ADHD, as she does seem hyperactive, and Konata from Lucky Star is the best example of an aspie otaku, in my opinion.