Game of Thrones is certainly a show that loves to include dramatic twists - from the first season when HBO shocked audiences by killing off what appeared to be the main character (Ned Stark), to the reveal that Littlefinger poisoned the Hand of the King Jon Arryn, to Varys' secret support of Daenerys... the list goes on, and it doesn't look like it's going to stop growing in the final season.
Of course, one of the biggest twists in the series so far has been the reveal that Jon Snow is not actually the bastard son of Ned Stark, but the trueborn son of Rhaegar Targaryen and Lyanna Stark - and heir to the Iron Throne. Of course, Jon isn't the only character in the series who may not be quite who he seems. Including a few mysterious book characters (who have shown up in the series), these are eight characters who might not be quite who they seem... and no. Not all of them are secret Targaryens.
Meera Reed is a relatively minor character in the Game of Thrones world - the elder daughter of Howland Reed, sister to Jojen Reed, and whose entire storyline in the show thus far has been to get Bran Stark North of the Wall... and then back to Winterfell again. However, fan theories suggest that there is more to this young woman than meets the eye. It's possible that Meera Reed is actually a Targaryen - and the twin sister to Jon Snow!
This theory is based on the idea that Lyanna Stark had twins, and that while Ned Stark took one baby, Howland Reed took the other (as the only other survivor of the Tower of Joy).
Unlike some of our secret Targaryens, this fan theory will make no difference to the outcome of Game of Thrones, even if it turns out to be true... because Qhorin Halfhand has been dead for a few seasons. However, this incredibly skilled swordsman and Ranger of the Night's Watch could well be Arthur Dayne, the Sword of the Morning.
For those fans who haven't read the books, Arthur Dayne was one of the most skilled swordsmen in Westeros, and one of the Kingsguard Knights who protected the Tower of Joy. In the series, Arthur Dayne is shown to be killed at the battle of the Tower of Joy, but in the books, there's a possibility that the swordsman escaped... and fled to the Night's Watch. This theory pulls from lots of smaller details in the books, but the basis for it is that Arthur Dayne would have been able to slaughter Ned, but that he is honorable - and chose the Night's Watch to serve the realm, where he became a brilliant (ambidextrous) Ranger. It would also mean that his decision to sacrifice himself to help Jon Snow could be based in an awareness of who Jon really is...
Bran Stark actually appears on this list twice, and his first entry is as Bran the Builder - the ancestor who founded House Stark, who built Winterfell, and who (according to Old Nan) may also have been the original Builder of the Wall. This theory posits that Bran Stark, as the Three-Eyed Raven, uses his warg/greenseer ability to time travel (sort of) in order to go back in time and build the wall.
Several small details back this up, from lines in the original novels such as "Sometimes Nan would talk to him as if he were her Brandon, the baby she had nursed all those years ago, and sometimes she confused him with his uncle Brandon, who was killed by the Mad King before Bran was even born. She had lived so long, Mother had told him once, that all the Brandon Starks had become one person in her head", or an image in Histories and Lore of Bran the Builder on a stretcher, just like Bran Stark.
What if all the major contenders for the Iron Throne, Jon, Daenerys, and Cersei... are all Targaryens, and this is a secret Dance of Dragons Round 2 situation? One theory suggests that Cersei and Jaime, rather than being the children of Joanna and Tywin, are actually the children of Joanna and Mad King Aerys. It's established that the Mad King had a thing for Joanna (and apparently took 'unwonted liberties' during her bedding ceremony) - and some have theorized that at some point, Aerys raped Joanna, leaving her pregnant.
This theory is backed up by the very Targaryen way that Jaime and Cersei act; from their incestuous love to their pale hair (which, admittedly, would be a Lannister feature too), to their determination that borders on madness.
Like the Arthur Dayne/Qhorin Halfhand theory, this theory isn't going to have an impact on the show, even if it turns out to be true... because like Qhorin, Mance Rayder is no longer with us in the world of Westeros. The King Beyond The Wall was said to have been left with the Night's Watch as a baby, but some fans believe that this is a lie, and Mance was actually Rhaegar Targaryen.
Rhaegar was supposedly killed at the Battle of the Trident, but this fan believes that whoever was actually killed there was an imposter, allowing Rhaegar to go into hiding with the Nights Watch, and then to leave it and become the King Beyond the Wall. There are certainly some holes in this theory, but it would still be nice to think that Jon Snow managed to meet, and respect, his real father before he died.
The second theory about the potential secret identity of Bran Stark is that he is actually the Night King. Like the theory that he is Bran the Builder (the two theories can even be combined), this theory relies on his powers and ability to time travel. The basis of the theory is that Bran, on seeing how powerful the White Walkers have become, attempts to go back in time and stop them before they reach their current strength.
This is why the Mad King went mad, hearing voices saying to 'burn them all'... the voice of Bran Stark, using his Three-Eyed Raven powers to whisper to him to burn the White Walkers and the bodies of the dead. However, after several failed attempts, Bran went back to the creation of the first White Walker... and got stuck there. The fear that Bran will spend too long in visions/the past/warging and be lost is one that has come up time and time again, and it finally happens - Bran gets lost warging into the body of the first White Walker, becomes the Night King, and that is what gives him such incredible powers.
Everyone in Westeros is secretly a Targaryen... or that's how fan theories sometimes feel. This theory claims that Samwell Tarly is actually the son of Rhaegar Targaryen and Elia Martell. This might seem impossible, given the fact that most of Westeros believe that when the Mountain killed Elia Martell, he also murdered her children - but it's possible that he actually murdered a random child, and that her real son (Aegon Targaryen) was spirited away by Varys.
Varys then gave the baby to the Tarlys, intending to raise him to the Iron Throne later in life. However, this plan fell through, he became a Daenerys supporter, and this is the real reason that Sam's 'father' sent him to the Night's Watch. Not because he was a coward, but because he's not a Tarly at all.
Finally, we have a fan-favorite theory; that it is Tyrion, not Jaime/Cersei, who is actually the son of Mad King Aerys and Joanna. This theory is similar to the one that would make the Lannister twins Targaryens, but has a little more to back it up. For one thing, if Tywin was aware that Tyrion was not his son, it would go a long way to explaining why he hated him so much. Yes, his mother died in childbirth and he is a dwarf, but any reasonable man would see that these are not things that Tyrion did intentionally. However, hatred of a bastard son of the man who raped his wife... now that makes more sense.
In the books, Tyrion also has much paler hair than his siblings, and one black eye - which suggests that he has something else (something Targaryen) going on in his blood. His fascination with dragons and abilities with Daenerys' dragons also point toward him being a Targaryen, as they are traditionally (pretty much) the only House able to become dragonriders. This would make Tyrion the third head of the Dragon... and as a fan favorite, this is an outcome that plenty of viewers still want to see.