I'd advoided this thread cause of it's daunting size, but I just finished reading the hundred-odd posts and wanted to add some things about the various theories floating around in here.
In relation to the whole Rhaegar-Lyanna thing, I've been wondering about the timeframe. How long did Robert's rebellion last? I think it was a year or so, but I couldn't say for sure. And was it sparked by Rhaegar's 'kidnapping' of Lyanna? When and where did this happen? That's something that has never been mentioned, as far as I can remember. I know Aerys's execution of Lord Rickard and Brandon was also a factor in the rebellion - were they at King's Landing in response to Lyanna's kidnapping? The rebellion seemed to come to an end at the Tower of Joy, with Lyanna dying - presumably giving birth to Jon. If it was a year from go to woe it would mean she fell prenant three months into the war and after being kidnapped (not earlier, as you'd assume were she being raped at Rhaegar's will). That would also mean Robert believed Lyanna was raped by Rhaegar for twelve straight months - which would certainly account for his Targaryen anger issues. I'm not sure what I'm getting at here, just something in the way it unfolded and the timeframe niggles at the back of my mind. Was hoping someone else might be able toscratch it...
That Rhaegar loved Lyanna is probably true. Have just started rereading the series, and in Dany's first chapter she mentions Rhaegar dying at the Trident 'for the woman he loved' - and I'm guessing she didn't mean Elia. And this info had to come from either Viserys or Raymun Darry, either of whom would probably know Rhaegar's feelings (the Darry's seemed pretty close to the Targaryens). And then there's the bit at the tourney at Harrenhal - an event that seems at the heart of a lot of things. Whether she loved him back? Ned 'had lived his lies for fourteen years' and this I think is probably the chief one.
I was really keen on the Rhaegar and Lyanna as Jon's parents theory for a long time, but I've started to go cold on it. Not sure why. Just a feeling I get - seems a little obvious for Martin. What of Ashara Dayne, whom Catelyn thought was Jon's mother, and Wylla, who Robert (and I think Edric Dayne) believed to be Eddard's other love? Convenient lies to cover Jon's true parentage, or the truth? The timeframe of Ned and Ashara being Jon's parents also confounds me (did nine months pass between the time Ned bought her Dawn and when she threw herself off the cliff? Catelyn must have had good reason to think so...).
But something someone else mentioned on this thread (sorry, I can't remember who - it was a good hour or so ago now I read it) started a new thought in my mind. They said the Daynes were descended from Targaryens from the Blackfyre line, which would mean that if Ned and Ashara were Jon's true parents, he'd still have Targaryen blood... It would also account for another problem I had - why Jon had no Targaryen traits - the silver hair or violet eyes, which, if he were the son of Rhaegar and directly in the Targaryen line, he'd probably have. I think Martin would take perverse pleasure in making us think R+L=J and then springing the truth - truth that he revealed in the first hundred pages.
Another theory I was toying with was that Aegon might not be dead - that the baby might have been switched before the Lannisters took King's Landing. After all, the poor thing had his head dashed against the nearest wall, so positive identification would have been a problem. Where he'd be now, I couldn't say - but the Dayne thing got me thinking again. The Daynes are bannermen to Dorne. Elia was a princess of Dorne. My question - how old is Edric Dayne? And what role is he going to play?
Wow, that was a long post. My apologies... but I'd love to here anyone else's opinions on these matters. Though mostly I just wish A Feast of Crows would come out...