I guess after the June 26th finale and the reveal that Jon Snow was actually born to Lyanna Stark and is not at all Ned Stark's bastard, we were still supposed to be questioning who Jon's father could possibly be... While I realize some non-book readers and GoT watchers are catching up, I really don't see how there was any question. SPOILER WARNING: His father is the beloved (yep, unlike his father Rhaegar was beloved by most) prince is the father of Jon Snow. HBO even supplied us with this wonderful and confusing map of enemies, parentage and such.
For those of you who know all of the characters like the back of your hand (or even if you don't), I just want to point out that the Rhaenys and Aegon they refer to, were Rhaegar and Elia Martell's children. Not Aegon the Conquerer and his sister Rhaenys Targaryen. I did a double-take for that so I thought I would mention it.
If you'd like to know more about Rhaegar Targaryen he looked a lot like his brother and sister, Daenerys and Viserys. He was very good looking with the platinum hair and violet eyes of the Targaryens and he played the harp. He was married to Oberyn and Doran's sister Elia and had two children with her whom he named after Aegon the Conquerer and one of his sister wives Rhaenys. In later years he did not get along with his father, mainly because his father went mad after being kidnapped and became paranoid of his son (and everyone else). Rhaegar did actually think about deposing his father before the rebellion started, especially after Aerys started killing people with wildfire without first giving them a trial therefore triggering a rebellion. (And because of all the other crazy things the Mad Kind did such as not bathing or cutting his hair or fingernails). Rhaegar had a touch of the Targaryen madness, though nowhere near the amount his father had. He believed he would fulfill a prophecy by having a boy and two girls who would take up the names of his ancestors the Conquerer and his sister wives, Rhaenys and Visenya. As stated above, his arranged marriage to Elia Martell produced two offspring, but after Elia had a miscarriage the maesters said she would never have another child. That is when Rhaegar turned to Lyanna Stark. At a famed tournament, Rhaegar named Lyanna Stark the queen of love and beauty instead of his wife. Some time after (whether you believe he kidnapped her or she went willingly) he and Lyanna ended up in the Tower of Joy and a baby was made. I tend to believe Lyanna ran off with Rhaegar. She told Ned she did not love Robert and she knew he would never be true to her. She was wild and free, even if that freedom was the last nail in the proverbial coffin. The Mad King had killed Brandon and Rickard Stark for no reason and very brutally, then demanded that Jon Arryn kill his wards, Ned Stark and Robert Baratheon, all while Rhaegar sought to depose him, but he ran off with Lyanna Stark instead. So, that leaves us where we are today. And while many on the internet have been theorizing what Jon's Targaryen name would be, let me remind you that Rhaegar believed he would have another girl. He already had an Aegon and a Rhaenys (therefore Jon wouldn't have been another Aegon) so Jon should've been a Visenya if you want to get technical. So, why don't we just leave Jon as Jon. Though it doensn't hurt to theorize while we're on break. And, he's still a bastard since his parents weren't married (unless in secret) and are not alive to legitimize him. That's a whole other issue entirely...
