The R+L=J theory is much older than some may think.
It dates back to 1997. Yes, that’s correct, it is not a typo.
Back in 1997, A Game of Thrones was the only book that was already released, so the level of knowledge readers had was roughly that of season one plus some background information from the book that didn’t make it into the show.
In September, 1997, a user going by the name Rodrick Su posted a theory that was almost identical to our R+L=J formula to the usenet group rec.arts.sf.written.
Jon Snow’s parent. It is wholely consistent that Jon Snow is the offspring of Rhaegar Targaryen and Lyanna Stark. Ned probably keep this a secret because Rober Baratheon is obsess with killing off all Targaryen, especially any offspring of Rhaegar.
If Jon Snow is a Targaryen, then by tradition, he is the most likely mate to Daenery, being that she is his aunt…
Here is the original post archived on google groups. The thread contains a few more interesting theories
It should be noted, that reading the books makes theory forging easier in my opinion. The reason for this is the vast amount of background information that very often does not make it into the TV show, simply because it would bloat a season to 20 or more episodes and is generally difficult to include without having some kind of “narrator” or extensive dialogues discussing past events.
GRRM has a habit of describing things with much attention to detail and his first book makes no difference. We learn quite some things about Robert’s rebellion, the Targaryen and many other events that are either completely absent from the show or get only scratched on the surface. The TV series concentrates more on current events and does not always explain the reasoning behind