@Neyjour :
I think you're right regarding my last 3 rec : Densha Otoka male lead is an otaku, pretty shy as you said, but not really an eccentric. yet his way of life makes him look like an outcast.
regarding Dokushin Kizoku, the male lead is a bachelor proud of his condition and telling what he really thinks to other people. that lead him being avoided. he has some habits, but that doesn't really make him an eccentric in the way you may want.
as for Nazotoki, the male lead is not really an eccentric, though he says what ever he wants to the woman he is working for.
When thinking more about it, those dramas are probably not what you want. I do recommend the three of them though, they are quite good. for Densha otoko, i'd rather the drama over the movie.
By the way, thanks for the thread, i would take a closer look at that list you're making, i like eccentric leads as well!