Realistically the Starks no longer have a grasp at the throne. Robb's armies are scattered, many going over to Stannis. Bran has no interest in the throne, nor does Sansa or Arya really. Rickon? Lawl. But realistically I think the war is over from a Stark perspective.
The Lannisters? The prophecy says that Cersei's children will die before her, but she will die by her brother. Let's assume that leaves Tyrion and Jaime. Regardless of which one did the killing, the other isn't fit for the throne - either because they're the head of the King's Guard or because they're a criminal whom nobody loves. And despite his shadow loooking like a King, do you think Martin really will put Tyrion on the throne, despite him being his and the fans favorite - GRRM is too smart. Besides, whomever sits on the throne will likely be a miserable fuck who has lost much and Tyrion doesn't really have much or anyone to lose. Besides, there's only one way he's able to sit the throne: marriage to either Margaery or Dany.
How fucking hilarious would that be if Tyrion married Cersei? "The Targaryans always married brother to sister..." and due to how much they hate each other? God, that would be awesome. Then Tyrion kills Cersei and is the kind, intelligent, and just king the world needs.
So let's take the Lannisters and Starks off the table. The next level down is the Targs and Tyrells. I'll start with the Tyrells: Marg probably won't survive and has no children. There, Tyrells out of the picture. Also note: GRRM is a fan of "threes" but not "fours". The dragon has three heads, Dany's prophecies are all in threes and the bottom line is that Margaery married three kings and will not marry a fourth.
On to Targs: We have Dany and possibly fake Aegon (and Tyrion?). Dany looks to be the one going for the throne and who has the backing of her dragons. It's almost like everything is working like clockwork for her to be sitting the throne. We as readers expect this; hell some of us talk and debate as if her succession is obvious. GRRM doesn't really give us obvious as I stated above when discussing Tyrion. What if she suddenly doesn't want it? What if she gives up and goes on to live in that little house with a red door she dreams of? What if she never even reaches the shores of Westeros, but is fine with that? Or dead?
Daemon Blackfyre was a legitimized bastard son and he founded the Blackfyres, so if Aegon is a Blackfyre as some suggest, he's STILL fit for the throne, though far far down the tree - as far as Robert was or farther. So Dany or Aegon or both could be on the throne, whether they married each other or someone else. But Aegon coming so late to the game, despite a couple hints that he survived would be interesting, but I'm getting a very Robb vibe from him....maybe his wedding might be red.
So back to Tyrion: if Tyrion is indeed a Targ he suddenly has ANOTHER reason to be on the throne. But in order to do that, his marriage to Sansa needs to be annulled and I don't believe divorce is an option. The only way to seperate Sansa and Tyrion is by death. What if Tyrion is a Targ and is able to prove that and accends the throne? What if he never meets back up with Tysha? Sansa wanted to be queen, she could be a queen for Tyrion, though not a happy one. Sounds bittersweet in a way: Tyrion would be able to fuck and whore his way across the kingdom, but that could cause another war and I wonder if he would force himself to stop that kind of behavior. If Dany were to marry Tyrion she would likely also be miserable, though who's to say despite fandom's insistance that Jon is the one she "mounts for love"? Maybe she finds a way to love Tyrion...would be an interesting ending.
And then there's Jon. We know that his death is a way out of the Night's Watch, but it's too easy. He would need to warg out to Ghost, Mel woudl have to heal his body, then warg back into his old body. But he's alive again and who says that removes his vow? He stays dead or warged long enough and he'll be replaced on the wall by another Commander, that's not the issue. But Jon is an honorable man. He may leave and join the war, maybe doing Mel's bidding like Mance did before, but I could see in the end him returning to the Wall. Even if he finds love again. There's a huge reason why the first three books focus so much on his vows (especially Got and SOS) and somehow I doubt George is going to forget how much he beat it into our heads that a NIGHTS WATCHMAN NEVER LEAVES HIS POST. Jon will not leave, he will not take a seat anywhere, even Winterfell, and definitely not on the big metal ass cooler that we call the Iron Throne.
TL;DR version:
My final thoughts on who could sit the throne in the end:
Tyrion with Dany
Dany and Aegon
Dany and Tyrion
Tyrion and Sansa
Of course my opinion could change daily as more insane theories come to mind. I really should just join Westeros.org and become their insane Patchface of prophecy.
Also, I know this is long and unedited, but it was written on the fly and I don't think anyone will read it regardless.