On Dany=Stannis:
I can't agree with the whole 'Dany = Stannis in a dress' thing - They may not be opposites, but they're very different.
Dany acts through her own sense of what's right and what's wrong as much as she can; it's often a case of emotion overriding the laws of the land. She follows her own moral compass.
Stannis, on the other hand (well, at least before he became Melisandre's puppet) does everything by the book, whether he likes it or not - he is 100% duty & law over personal choice. It's made pretty clear from Maester Cressen's nostalgia trips that he was like this as a child also; straight laced, solemn and dutiful to the point of having no one close to him. Maester Cressen pitied him for it.
Just because they'd probably both have freed the slaves doesn't mean they're the same; they'd have done it for completely different reasons.
On R+L=J:
I'd suspected that Jon might have been Lyanna's, not Ned's, but had never really thought it through to the point of realising that he was Rheagar's. This adds up very nicely.
As to Dany and Jon sharing the throne, I can't see it happening. I think he'll be a head of the dragon, but given Martin's style, I think it's inevitable that one of them will die. I'm not sure which would give the biggest emotional impact - my initial thought was that Jon would have to die, but it would perhaps make more sense for him to survive and rule rather than Dany, who doesn't really know Westeros. Also makes me think that the third head will be female (?).
Thinking about Jon, did Rhaegar take Lyanna as his (second?) wife? She loved him didn't she? I can't quite remember the details of all that. It would be interesting if Jon had been legitimate the whole time, eh?
I don't think the fact that he doesn't look like a Targaryen really matters (though it is interesting - as of Ned's natural children, only Arya shares the Stark looks rather than the Tullys' suggesting a 'weak' Stark seed). The whole Targaryen fondness of inbreeding (as suggested earlier in the thread) would explain how they keep their 'look' despite having genetically recessive physical traits.
On Howland Reed=Guy Incognito:
Yes, Howland Reed is a bit of an enigma, eh? I think it's a given that he was the crannogman who won the tourney in the story.
Could it be that he either had or had been told of a Green Dream about the fight at the Tower of Joy. If, like Jojen, he knows the time and circumstance of his death - and knew that this wasn't it - he could have fought with a ferocity and disregard that could have allowed him to overcome supposedly superior opponents. Perhaps he used the crannogmen's knowledge of poisons as well. Might be a bit disappointing to learn that the Sword of the Morning died from an arrow in the foot though.
Ned's reticence to speak of what happened does suggest something underhand/darker though. Perhaps some kind of warging or other green art took place. I suspect that Ashara's death was suicide though, not murder.
I reckon, though, that Martin will save Howland Reed and these explanations until right at the end. I'd definitely agree with the possibility that Howland Reed has been hiding in plain sight the whole time, though. I'm trying to think of all the small, slight male characters who are possibilities. Do crannogmen have other distinctive physical traits other than their build?