**Edit in progress.**
Almost everyone is familiar with the Rosetta Stone. It was the key that unlocked ancient Egypt's hieroglyphs. In a similar fashion, the blue winter roses in ASoIaF help to unravel the mystery of Jon Snow's past, while also possibly providing some hints about his future.
The biggest misconception about the winter roses, imo, is that they symbolize (only) Lyanna Stark. There is some truth here, but she is only a part of the equation. I wouldn't go so far as to say the notion that 'Lyanna = blue roses' is a red herring. But, because the flowers are always presented in AGoT as relating to her, I do believe GRRM was intentionally leading the audience down a dimly lit path, so to speak.
Ned thinks about, remembers, or dreams of Lyanna in combination with winter roses on a handful of occasions. Yet it is not until his final chapter (XV) that we learn where Lyanna's roses came from. Ned remembered the moment when all the smiles died, when Prince Rhaegar Targaryen urged his horse past his own wife, the Dornish princess Elia Martell, to lay the queen of beauty’s laurel in Lyanna’s lap. He could see it still: a crown of winter roses, blue as frost. The fact that GRRM waits until Ned's final POV to reveal this to us is no accident. In fact, this juxtaposition of the start of Rhaegar and Lyanna's relationship in Ned's last chapter mirrors his memories of their deaths in his first chapter. In other words, GRRM begins with Rhaegar and Lyanna's deaths (their end), and ends with their beginning.
The significance of this reveal means that a first time reader must reconsider what the roses mean in story. These aren't just Lyanna's roses. These are Lyanna's roses that were given to her by Rhaegar. The QoLaB's crown is the source for all of Lyanna's associations with blue winter roses in ASoIaF. Due to the way GRRM structured the reveal, their origin is often overlooked or downplayed which leads to people mistaking the effect for the cause. It seems much more likely to me that the crowning is what caused the later affinity for, and association with, roses.
Before getting started, it's worth noting what blue roses tend to mean in the real world. For example: "The meaning of the blue rose is about mystery [as in; who is Jon Snow's mother?] or attaining the impossible. The blue rose is also used as a symbol of love at first sight [R+L?]. The blue colouring also represents royal blood [which Jon receives from his father] so it can represent splendour and regal majesty."
“I was with her when she died,” Ned reminded the king. “She wanted to come home, to rest beside Brandon and Father.” He could hear her still at times. Promise me, she had cried, in a room that smelled of blood and roses. Promise me, Ned. The fever had taken her strength and her voice had been faint as a whisper, but when he gave her his word, the fear had gone out of his sister’s eyes. Ned remembered the way she had smiled then, how tightly her fingers had clutched his as she gave up her hold on life, the rose petals spilling from her palm, dead and black. After that he remembered nothing. They had found him still holding her body, silent with grief. The little crannogman, Howland Reed, had taken her hand from his. Ned could recall none of it. “I bring her flowers when I can,” he said. “Lyanna was... fond of flowers.”
- Eddard I
As they came together in a rush of steel and shadow, he could hear Lyanna screaming. “Eddard!” she called. A storm of rose petals blew across a blood-streaked sky, as blue as the eyes of death.
Her eyes burned, green fire in the dusk, like the lioness that was her sigil. “The night of our wedding feast, the first time we shared a bed, he called me by your sister’s name. He was on top of me, in me, stinking of wine, and he whispered Lyanna. “
Ned Stark thought of pale blue roses, and for a moment he wanted to weep. “I do not know which of you I pity most.”
He was walking through the crypts beneath Winterfell, as he had walked a thousand times before. The Kings of Winter watched him pass with eyes of ice, and the direwolves at their feet turned their great stone heads and snarled. Last of all, he came to the tomb where his father slept, with Brandon and Lyanna beside him. “Promise me, Ned, “ Lyanna’s statue whispered. She wore a garland of pale blue roses, and her eyes wept blood.
Let's revisit The Moment When All the Smiles Died, from Eddard XV, because there is an addendum which belongs here, I think.
Ned remembered the moment when all the smiles died, when Prince Rhaegar Targaryen urged his horse past his own wife, the Dornish princess Elia Martell, to lay the queen of beauty’s laurel in Lyanna’s lap. He could see it still: a crown of winter roses, blue as frost.
Ned Stark reached out his hand to grasp the flowery crown, but beneath the pale blue petals the thorns lay hidden. He felt them clawing at his skin, sharp and cruel, saw the slow trickle of blood run down his fingers, and woke, trembling, in the dark.
Promise me, Ned, his sister had whispered from her bed of blood. She had loved the scent of winter roses.
But there were others with faces he had never known in life, faces he had seen only in stone. The slim, sad girl who wore a crown of pale blue roses and a white gown spattered with gore could only be Lyanna.
- Theon XI
A blue flower grew from a chink in a wall of ice, and filled the air with sweetness.
-Daenerys IV (HotU)
The Song O' the Winter Rose; Bael, Rhaegar, Mance, R+L=J:
Lately there has been a push by some to argue that Mance Raydar is actually Rhaegar Targaryen in disguise, hiding and waiting for the coming battle with the Others. This is based on a number of parallels between the characters that can be found in the ASoS, Jon I, when Mance and Jon first meet.
In ADwD, Mance suddenly seems to have lots of parallels with a different character, Bael the Bard. But I don't believe that this is because Mance is really Rhaegar, and Rhaegar is trying to follow in Bael's footsteps. Rather, I think GRRM is reinforcing the connection between Rhaegar and Bael, via Mance. A connection which already existed thanks to blue winter roses, Stark maidens, and their sons.
As to the parallels between R+L=J and the song o' the winter rose. At their core both stories feature singers who steal Stark maidens and give them sons. To that you can add, for example, that Rhaegar was the crown prince, while Bael went on to become the King-Beyond-the-Wall. Both stories also feature lots of death.
I believe it is supposed to prompt anyone who doesn't already know about R+L=J to connect blue roses to Stark maidens and their sons. In other words, it's a clue that Jon has Stark blood through his mother, not his father; i.e., Jon is half-Stark, but Ned is not his father.
This is, of course, the BtB story as it pertains to R+L=J. There are almost certainly other events that are foreshadowed by that tale.
Thanks for reading.
Edited by J. Stargaryen, Yesterday, 11:12 AM.