Let's assume that Jon Snow is the product of Lyanna Stark and Rhaegar Targaryen.
How will the reader ever find this out? So far the prevailing theory has been that only Howland Reed will be able to reveal this secret to the audience / other characters.
There are a few other possibilities though, aren't there?
Septa Lemore is actually Ashara Dayne, and she can reveal that Jon Snow was brought by Ned Stark from the Tower of Joy (implying that he is Lyanna's son) to Starfall, where he was nursed by Wylla.
Bran sees something in a godswood-flashback, but doesn't really understand what's going on (the reader, however, will understand the implication).
Jon's true parentage is never revealed outright.
Any other possibilities?
EDIT: From the comments...
4. Barristan Selmy, or other Kingsguard members, could know that Lyanna was pregnant/expecting at the Tower of Joy.
5. Wylla could rule herself out as a mother and perhaps confirm that Ned Stark brought Jon Snow to Starfell from the Tower of Joy.