SPOILER ALERT!! Don't read the article or watch the video if you haven't seen Season 6 yet.
Finally the wait is over and the Season 6 finale has confirmed that Jon Snow is indeed Rhaegar Targaryen's son and not Ned Stark's bastard. The scene of Tower of Joy where Lyanna whispered the theory we have been speculating since a decade and confirmed that he is a Targaryen was a treat for the fans.
Now that we all know that he is one of the three heads of the dragon, a YouTube user hurleybird collected all the scenes right from Season 1 to Season 6 that hinted at the true parentage of Jon Snow and arranged them in a spectacular way. Check out this awesome super-edited video and relive the R+L = J theory.