Various spoilers ahead.

This will be resolved based on the future asoiaf books, sample/leaked chapters or author's notes if it becomes clear that the notes are all we're ever going to get. If the series is officially completed by an author other than George R. R. Martin, those books will also count. If the series is completed (or forever remains incomplete) but there's no definitive answer one way or another, will N/A or resolve to probability.

Clarification:

* R+L=J: Jon Snow is the son of Rhaegar and Lyanna.

* The notorious Pink Letter ostensibly by Ramsey Bolton is written by anybody other than him (presumably to manipulate Jon).

* Jojen-paste: Children of the forest have sacrificed Jojen Reed and the mysterious magical paste that Bran Stark eats is at least partially made of Jojen.

* Mad Queen Dany: by the end of the story Daenerys Targaryen becomes mad/evil/highly unsympathetic, a de-facto antogonist and ends up commiting greater atrocities than expected. Does not have to be literally insane. The way it went in the show would count as "Yes".

* King Bran: in the end, Bran Stark ends up ruling what remains of Westeros. (Edit: has to be an official ruler known to everyone, Bloodraven 2.0, Evil Vizier, Sorcerer secretly controlling events from the shadow/mindcontrolling the king doesn't count.)

* Shireen burnination: Shireen Baratheon ends up sacrificed by Melisandre via burning to death, with or without approval of King Stannis.

* Aegon is a Blackfyre: Young Griff (supposedly Aegon Targaryen, son of Rhaegar) is secretly from the Blackfyre family, an offshoot of the Targaryen line and is therefore, an imposter.

* Nightlamp: Stannises battle plan is to lure the Bolton/Frey forces on the surface of the frozen lake and then make the ice break, drowning them.

* Lemongate: there's an inconsistency between Dany remembering seeing a lemon tree in Braavos and the repeated idea that lemon trees do not grow there. The theory is that this implies that she had spent her childhood elsewhere as a part of some secret plot.

* Bolt-On: Roose Bolton is an undying creature who stays alive by possessing his heirs, generation after generation.

* Somebody is Euron: some character from books 1-5 is secretly Euron Greyjoy in disguise/magical glamour or is posessed and controlled by Euron.

* Time-travelling fetus: Tyrion Lannister is a time-travelling son of Daenerys Targaryen and khal Drogo.