In the Season 6 finale of Game of Thrones the popular R+L=J fan theory was finally confirmed. As many fans suspected, Jon Snow is actually not the son of Ned Stark, but is in fact the son of Lyanna Stark and supposedly Rhaegar Targaryen, Daenerys' brother. However, some fans are questioning what exactly Lyanna whispered to Ned that we couldn't hear. Although most fans believe Rhaegar is Jon's true father some wonder if it really was Rhaegar's name that Lyanna whispered to Ned.
Earlier in Season 6, fans were taken to the Tower of Joy when Bran warged there with the three-eyed raven. Fans thought they'd finally see the truth about who Jon's parents really are but just as Bran was following his father into the Tower he was pulled out of the vision much to fans disappointment. It wasn't until the finale that Bran revisits the past and sees his father enter his Aunt Lyanna's room, where her bed is covered in blood. Ned goes to his sister and she tells him she doesn't want to die and that she tried her best to stay alive. She then has him bend down and whispers in his ear. Most fans believe this is when she confessed that she had a son with Rhaegar. When Ned pulls away she asks him to protect him, meaning Jon.
Even so, as Game of Thrones fans know, sometimes things aren't always as they seem and even though we all want to believe it, Rhaegar's name might not be what Lyanna said. But who else could be Jon's father? It can't be Robert Baratheon, because if it was there'd be no reason to keep Jon's true parentage a secret, and Rob would've undoubtedly been happy to have a child with Lyanna, who he loved. Rhaegar seems to be the only person that makes sense in this situation since he's the one that kidnapped her or ran away with her (depending on what you believe).
It seems unlikely that the showrunners would finally confirm this highly anticipated theory just to pull the rug out from under fans. Plus, it's been made clear time and time again that Jon Snow is important to the Game of Thrones story. The fact that he was brought back to life after so many other characters have died forever makes it clear that he plays an important role. Many fans believe the fact that he is both a Stark (ice) and Targaryen (fire) is what makes him the hero Westeros will need when the White Walkers finally come, and there's no doubt that whatever Lyanna whispered to her brother was a confirmation of that.