The entire Jon reveal is completely lost on me as I absolutely forget about who any of those people were.. who is the sister, who was her husband, what marriage was annulled? These people were introduced so long again that I'd have to revisit a family tree online to get a handle on it.
The sister was Ned Starks sister. The husband was one of the children of the Mad King, Dany had two brothers, him and the guy we see with her in the earlier seasons. Obviously there was some age difference.
So Neds sister and Danys older brother made Jon Snow, therefor Dany is his aunt/he is her nephew. So he both has the blood that makes those people special when it comes to dragons and shit, and if it even matters any more, has some sort of rightful claim to the throne.
Seeing as how a big old war was going on back then, Jon was in danger of being killed, so Ned pretended his sisters child was his own bastard child.