Oh yeah, that's a big one. I think a whole lot of people just assume it as truth now. There's a lot that point to it. Fortunately, GRRM doesn't seem to be the type to change a twist if people figure it out early (so, at least, if L+R=J turns out untrue we can fill confident it was always not true
).
Sort of a companion theory is that Aerys the Mad King is Tyrion's true father. Basically, Aerys took certain liberties with Tywin's wife and became pregnant with Tyrion.
The end theory here is that Jon, Tyrion, and Daenerys are the three heads of the dragon (being all three Targaryens) and all three represent Azhor Azhai reborn. Something like that. It'll be exciting seeing if its true.