This is a summary, rather than a quote from the book.
Jon tells Sam of a recurring dream he has of Winterfell. He dreams he is walking in a long, empty hall in the castle, his voice echoing around him and no one is answering. He is looking for someone, but he isn't sure who, sometimes it is his father, sometimes Robb, or Arya, or even Benjen. But he never finds anyone, the castle is always empty. Even the ravens are gone, and the stables are full of bones. It scares him, and he runs around looking for someone. Then he finds himself in front of the door to the crypts, and he knows he has to go down there, but he doesn't want to. He's afraid of what is waiting for him. Not the old Kings of Winter, but something else. He screams that he is not a Stark, that it isn't his place, but it is no good and he feels he has to go down, so he starts, with no torch to light his way. It gets darker and darker, until he wants to scream, and then he wakes up.
This is a very interesting dream, and is perhaps prophetic in a way. It seems there's some secret in the crypts below the castle of Winterfell which has to do with Jon, no matter how much he protests. He knows he's looking for someone, but he never finds any of the people he expects -- instead he is inexorably led to the crypts. Could it be that the person he seeks is there? If so, this is strong support for the theory that Lyanna Stark -- entombed there besides her father and eldest brother -- is Jon's mother, and that she is the secret that draws him in his search.
Another possibility that has been put forward is that the dream signifies that Jon is being drawn towards a darker future, and that his descent into darkness doesn't bode very well for the future. Of course, these interpretations are not mutually exclusive, so both meanings might be intended.