"I dreamed about the crow again last night. The one with three eyes. He flew into my bedchamber and told me to come with him, so I did. We went down to the crypts. Father was there, and we talked. He was sad."
"And why was that?" Luwin peered through his tube.
"It was something to do about Jon, I think." The dream had been deeply disturbing, more so than any of the other crow dreams.
If Bran really spoke to the shade of his father, it may be that the spirit of Eddard tried to reveal that Jon was not Bran's brother. This would certainly disturb Bran, because it's repeatedly noted that Jon is his favorite sibling. Another possibility is that the spirit of Eddard knew something of events to come and tried to tell Bran of the dangers that Jon would be facing. On the whole, we prefer the former interpretation.
The three-eyed crow has been revealed to be Ser Brynden Rivers, once known as Bloodraven, a former Lord Commander of the Night's Watch and one of the Great Bastards of King Aegon IV. He has lived long beyond his natural lifespan, merged with the weirwoods, with the intention of helping to save the world of men from a coming threat.