After the last 2 episodes I think it is obvious that Jon Snow is the son of Ned's sister and Danerys's brother Raegar (?). They've dropped too many hints now between the books and the show for it to be anything else. Plus, the only way Ned would take on the shame of having a baseborn child would be to save his sister of the same shame. I actually think Jon Snow and Danerys make up 2 of the 3 dragon heads that keep on coming up. My guess is that the 3rd one has not been introduced on the show though has been in the books).
Just my opinion but it does seem to be getting more and more likely.