Okay, so I decided to compile the reasons why I think they will be together.
"Her silver was trotting through the grass, to a darkling stream beneath a sea of stars."
"A corpse stood at the prow of a ship, eyes bright in his dead face, grey lips smiling sadly."
She dreams of sex with a corpse in ADWD:
"Beneath her coverlets she tossed and turned, dreaming that Hizdahr was kissing her...but his lips were blue and bruised, and when he thrust himself inside her, his manhood was cold as ice."
So to me that implies at the very least that the she will be sexually intimate with the men in the bride of fire sequence.
"A blue flower grew from a chink in a wall of ice, and filled the air with sweetness."
. . . mother of dragons, bride of fire . . .
. . . three heads has the dragon . . .
. . . three fires must you light . . . one for life and one for death and one to love . . .
. . . three mounts must you ride . . . one to bed and one to dread and one to love . . .
. . . three treasons will you know . . . once for blood and once for gold and once for love . . .
The mother of the direwolves was huge:
"But it was the size of it that made him gasp. It was bigger than his pony, twice the size of the largest hound in his father's kennel."
Ghost is a male so he should be even bigger.
Dany hears a wolf in the distance in ADWD. I believe that this is a subtle clue.
"Off in the distance, a wolf howled. The sound made her feel sad and lonely, but no less hungry."
Jon thinks that Val and Ghost look like they belong together.
"Then Ghost emerged from between the two trees, with Val beside him. They look as though they belong together...It had been a long while since Jon Snow had seen a sight so lovely."
There is a scene which IMO is subtle foreshadowing where Val's hair looks like Dany's. I don't think that this is a coincidence.
"The light of the half-moon turned Val's honey-blond hair a pale silver and left her cheeks as white as snow."
Jon specifically wants a son. Dany lost one. Dany's MMD curse is coming true in ADWD. She just needs to have a living child.
"I would need to steal her if I wanted her love, but she might give me children. I might someday hold a son of my own blood in my arms. A son was something Jon Snow had never dared dream of, since he decided to live his life on the Wall."
IMO, Val is misdirection. He thinks that Val would be a worthy wife but his actual wife will be Dany.
"A nubile girl, not hard to look upon. Good hips, good breasts, well made for whelping children." All true enough, but the wildling woman was so much more...She may not be a princess, but she would make a worthy wife for any lord."
People use this quote Jon said about Axell Florent to show that they aren't compatible.
"What sort of man can stand idly and watch his own brother being burned alive?"
If anything I think this will be a joke on Jon. The woman he loves will have done this. This is like when he told Arya that bastards can't harm princes in reference to Joffrey.
Now, I understand that this one has no evidence but I believe that the face she can't see is Jon's.
"Sometimes she would close her eyes and dream of him, but it was never Jorah Mormont she dreamed of; her lover was always younger and more comely, though his face remained a shifting shadow."
Feel free to disagree. I know many hate this pairing.