Close variations on many of the storylines about the Nightfort are now true of Winterfell:
The Nightfort had figured in some of Old Nan’s scariest stories. It was here that Night’s King had reigned, before his name was wiped from the memory of man.1 This was where the Rat Cook had served the Andal king his prince-and-bacon pie2, where the seventy-nine sentinels stood their watch3, where brave young Danny Flint had been raped and murdered4.
This was the castle where King Sherrit had called down his curse on the Andals of old5, where the ‘prentice boys had faced the thing that came in the night6, where blind Symeon Star-Eyes had seen the hellhounds fighting7. Mad Axe had once walked these yards and climbed these towers, butchering his brothers in the dark8.
All that had happened hundreds and thousands of years ago, to be sure, and some maybe never happened at all. Maester Luwin always said that Old Nan’s stories shouldn’t be swallowed whole. But once his uncle came to see Father, and Bran asked about the Nightfort. Benjen Stark never said the tales were true, but he never said they weren’t; he only shrugged and said, “We left the Nightfort two hundred years ago,” as if that was an answer.
Bran forced himself to look around. The morning was cold but bright, the sun shining down from a hard blue sky, but he did not like the noises. The wind made a nervous whistling sound as it shivered through the broken towers, the keeps groaned and settled, and he could hear rats scrabbling under the floor of the great hall. The Rat Cook’s children running from their father.
The yards were small forests where spindly trees rubbed their bare branches together and dead leaves scuttled like roaches across patches of old snow. There were trees growing where the stables had been, and a twisted white weirwood pushing up through the gaping hole in the roof of the burned kitchen. Even Summer was not at ease here. Bran slipped inside his skin, just for an instant, to get the smell of the place. He did not like that either.
1 Old Nan "would always end" her story of the Night's King by insisting that he was a Stark. He was finally "deposed" by his brother, who was the Stark of Winterfell.
2 Manderly brought the alleged Frey pies to the wedding feast for Ramsay and fArya.
3 I'm not sure of the match for this part of the story. These were 79 Night's Watch deserters who were sent back by the leader's father and then sealed into the Wall as punishment for desertion. Could the Stark kings and Lords in the crypt be the same as the 79 sentinels?
4 Jeyne Poole is disguised as Arya and is essentially raped by both Theon and Ramsay for the bedding and subsequent nights at Winterfell. She has not been literally murdered, however.
5 I don't know if the oath Ned makes in his cell at King's Landing would be the equivalent of Sherrit's curse.
6 The servants at Winterfell "face" Theon's sea coming over the walls of Winterfell and the rest of the horrors involved in Theon and Ramsay's occupation. Ramsay kills all the men who help rebuild the Great Hall.
7 There is a dramatic scene in the crypt where Shaggydog and Summer's giant shadows are cast against the wall by torch light while they seem to fight.
8 Theon could be Mad Axe, as he purports to butcher his "brothers," Bran and Rickon. Or the "Ghost" that seems to be randomly killing victims caught in the snow storm could be the equivalent of Mad Axe.
I don't know if Winterfell has an exact match for the Rat Cook. Theon violated Guest Rite when he was the Prince of Winterfell. He killed some people, but they were employees, not really guests. Manderly seemed to avoid violating guest rite when he made his pies. All the Freys who attended the Red Wedding might be part of the Rat Cook allusion, however, and some are now at Winterfell for the Bolton wedding.
My current thinking about horses is that they represent power - people who lose their horses lose power. Horses are also associated with the First Men, I think. So the Nightfort stable being replaced by trees is an interesting symbol; possibly a return to the time before the First Men had power there.
Of course, the most important feature of the Nightfort is the Black Gate, deep below the castle. It can be opened by a member of the Night's Watch. Does the Winterfell Crypt contain an equivalent door that allows people to cross to a cold, forbidden place? Did Hodor / Walder encounter that door in the exploration that struck him (relatively) dumb, years ago? Is that why he keeps saying this word that sounds like some kind of door? Wearing my puns and wordplay hat for a moment, I would also note that Hodor and odor might fit with GRRM's wordplay games. Bran says he (via the direwolf Summer) doesn't like the smell of the Nightfort. Maybe this bad smell represents a premonition about what will happen on the other side of the Wall, or maybe he is sensing that the door back at Winterfell should not be opened - it doesn't smell good to him.
Winterfell and the Nightfort are both ruins. The former is occupied by Theon and then Ramsay; the latter is taken over by Stannis and Selyse Baratheon, with permission from Lord Commander John Snow. Is Selyse a new "corpse queen"? Is Stannis a new Night's King? Are Ramsay and Jeyne Poole doomed to play out those same roles at Winterfell? Or do the new players all have to be Starks, as they were in Nan's version of the old story?