Clearly there will be spoilers (under cut):
I think that Jon Snow is going to ally with the Lannisters.
Thoughts on why:
First, the story itself is going to be a snooze if it's Daenarys-the Tyrells-the Martells-the Starks-Yara-The Iron Bank of Bravos-and-literally-everyone-else vs. um...Cersei and Qyburn (and undead Mountain? and Jaime, maybe?). The only way to even things up is to throw the Starks on the Lannister side, thus giving us a massive twist, with the bonus double awesome of a major conflict. (Not that the white walkers won't be cool, but I don't think they'll be all that exciting for more than maybe 2 episodes.)
Okay, but plot mechanics alone don't make for a good twist...but I think it's pretty plausible. Here's why...
First, I'm assuming that Cersei isn't freaking stupid enough to tell everyone, "GUESS WHAT I DID EVERYONE? I EXPLODED THE SEPT AND KILLED EVERYONE! MWAH HHAH HAH HAHAHHA!!!!" Because, even for her, that would be pretty freaking stupid. (And I'm guessing that when it finally is revealed that Jaime will kill her.) No one has blamed her for it (yet) on the show and why would they? All they know is that a massive exposion went off that killed a bunch of people, incuding Cersei's OWN FAMILY. (Kevin Lannister, aka head of the clan was there as was Lancel, the cousin she was made to do the walk of shame over. That's in addition to her children's graves, her father's grave, etc. etc.) I mean, SHE SUFFERED TOO! (Or at least she can claim she did if anyone accuses her.) So... why would she be blamed for it? The citizens of King's Landing didn't watch the epic intro to Season 6, Episode 10. All anyone knows is that she fortunately (unfortunately?) was in the Red Keep when the explosion went off.
(Heck, if she's super clever, she might even be able to blame it all on terrorist-Dany because, hey! The Mad King's daughter shows up and *suddenly* all the explosives that the Mad King buried under the city just happen to go off at a time that kills off most of the major families in the land? That sounds pretty suspicious. Not to mention that it would make a great plot twist. Dany returns and rather than everyone being all, "Oh, beloved mother and freer of slaves and rightful queen, we are so glad you've returned!" they're all like, "Go away terrorist scum!!!!")
So Cersei isn't going down for that, yet. And so she seems a reasonably sane ally. From Jon Snow's perspective, she's probably marginally worse than Dany because of the whole "Kill-Ned-Stark-thing", but he doesn't know what Dany is actually like + Joffrey can take most of the blame for Ned's death. (Cersei wanted to exile him to the wall, after all.)
Meanwhile, Jon needs to get that Dragonstone ASAP. (In fact, its reveal was a brilliant little plot twist because now he can't just hide in the North fighting the white walkers like he'd most like to do. HE HAS TO FIND A WAY TO GET DRAGONSTONE AS WELL AS DRAG IT ALL TO THE NORTH.)
Of course, he *could* ally with Dany...and my guess is that this will be his first step. He won't be able to go himself, since major war prep, but I'd guess that Ser Davos would be willing to act as his emissary. Ser Davos gets to Dragonstone and is instantly somewhat put off by Dany tearing down all those Stannis-banners and bad mouthing the Baratheons and claiming that she's the rightful queen (even though she just freaking GOT here, and literally knows NOTHING) and grumps a bit. Dany doesn't take the white walkers seriously, because literally no one who's seen them has. Between Davos being grouchy and Dany being arrogant, negotiations go poorly. Davos returns empty handed. (Or heck, if there's not time for that, then Jon sends a raven that gets lost or apprehended by the Lannisters or literally whatever.)
Now Jon is stuck in a crappy position. He doesn't want to ally with Cersei, but Dany's turned him down and Cersei is suddenly being rather reasonable seeing as she's only got her brother, a zombie, a mad scientist, and a really mad pirate (who wants to marry her, even though him having two hands probably isn't much of an incentive to her...). Maybe Jon even believes Terrorist-Dany rumors. Either way, he needs the obsidian and Cersei has some armies + a fleet. So they ally. He acknowledges Cersei as proper queen. She acknowledges him as King of the North (not like she cares about the place, anyway), he agrees to help her regain Highgarden (probably, since she needs the grain. Maybe she throws in some troops for the wall), she gets him his Dragonstone.
Sansa, of course, will throw a fit. (Remember that she knows what Cersei is like and probably isn't going to be so forgiving, unlike Jon who's going to find a way to blame Joffrey for everything once his alliance relies on a selective memory.) So Sansa will faff off with with Paetr Baelish, who really would like everyone to continue killing themselves. Suddenly the sides are even - the North-Euron-Jaime-Cersei vs. Dany-Tyrion-the Tyrells-the Martells-Yara-whoever I'm mising. It's an even fight and promises some pretty epic battles as well as some fantastic moral ambiguity.
What do you think?
(Further predictions - Cersei does everything in her power to legally adopt or marry Gendry, because he's the closest thing that there is to a legitimate ruler. Or if she doesn't, Daeneary's is going to do her best to get her mitts on those sweet, sweet arms that are all buffed up from decades of rowing.)