I've not got the book so I can't quote, but I read a very interesting passage from book one. It's when Ned's in the whorehouse with one of Roberts bastards. The phrasing is ambiguous: it talks of a "He" which could be Ned or Robert. It's something like this: "Ned reached out and touched the infants hair.Robert [..something about what Robert did or his bastards]. The hair felt like soft whatever, just like that of his firstborn."
The second half is either being said by Ned or of Ned. I think it's the latter, I think it indicates Robert had a son, that is somehow illegitimate, perhaps even by Lyanna somehow, that is VERY different to Joffrey. And Ned remembers that this firstborn, legitimate or not, had Roberts hair.
Has anyone followed this up and put out a sound backing as to how Jon could be Jon Baratheon? If there's a post about it please link, otherwise I'd love to hear some more evidence for or against.