Lyanna Stark.
After re-reading book 1 I came to this conclusion. Here is why:
* Rhaegar Targaryen ignored his wife and throw the flowers at Lyanna Stark after he won the jousting tournament. He later allegedly kidnapped her, according to Robert - but what really happened?
I think Rhaegar Targaryen had an affair with Lyanna Stark, who wasn't that interested in Robert Baratheon even though he was in love with her, since she knew that he was a cheater and would cheat on her. Rhaegar Targaryen captured her heart; when he stole her away, I'm betting it was because she was pregnant. When Ned Start goes to the Tower of Joy and fights the 3 knights with his team of 7, only he and one other guy survived, and when he found Lyanna she was in a "pool of blood". Why would she be in a pool of blood if she wasn't fighting?
Answer is obvious; she was giving birth to a baby. That baby was Jon Snow. She made Ned Stark promise her to keep the secret. The reason Ned had to keep it a secret was that Robert Baratheon was insane when it came to any Targaryen, even a baby, and would have killed "Jon Snow" had he know that it was the baby of his beloved Lyanna Stark and Rhaegar Targaryen. Therefore Ned took the secret to his grave to protect Jon's true identity.