This includes comics, anime, manga, short stories, novels, movies, cartoons, live action series, legends, narrative poems, myths, legends, ...etc
give it a good thought before posting.
I've made this on CV, but didn't last very long. http://www.comicvine.com/forums/off-topic-5/best-martial-artist-in-all-fiction-714461/
So read that thread, and if you got something to add, then please do. I'd love to hear. So far, I'm convinced that Yuujiro Hanma is the best.