Uncharted/WMG

Katherine Marlowe is also a descendant of Sir Francis Drake.

 * Marlowe takes the ring because she thinks she is the proper heir of Francis Drake. She doesn't like Nate because he's "unworthy" of the legacy and the name of Drake.

Katherine Marlowe is Sully's ex.

 * It's Sully. I was surprised that Elena and Chloe weren't exes when they first showed up.

Katherine Marlowe is immortal, or at least, hundreds of years old.
16th century English playwright Christopher Marlowe's mother was named Catherine, with some sources spelling it as "Katherine". He was also rumored to be a spy for Queen Elizabeth I, who had, among others, Sir Francis Drake as a part of her entourage. During his journeys, Drake, along with Marlowe, discovered the Atlantis of the Sands, the lost city in the Arabian desert, and found within it the Fountain of Youth. Katherine acquired the waters of the Fountain and used them to prolong her life indefinitely. The city was lost when Drake died, and now Katherine is trying to find it again, possibly to get more water (the effects of the Fountain may be finite) or to find her son Christopher (who may still be in the Atlantis of the Sands).

Taken from this IGN article.

Nathan's hair was behind everything

 * Its got a mind of its own, so it forces its host to steal things to sell for money so it can survive on hair care products. Its the only way I can answer why it never gets messed up or wet when it touches water or snow.

Nathan's health doesn't actually decrease in-game
Contrary to popular belief, it isn't Nathan's health that grows steadily worse as he gets shot: it's actually his composure. When he gets shot, he gets flustered, and as such runs a higher chance of actually being hit by the next bullet that flies his way. As the screen moves towards black and white, his cool steadily slips away until he finally loses the uncanny ability to dodge bullets fired at him by trained marksmen and falls squarely into their sights. Hence, he can be nearly killed a single bullet from Flynn, but shrug off the mountain's worth of metal that gets thrown his way. An interesting alternative, it isn't Drakes composure that decreases, its his luck. He's just lucky enpough that they keep missing him, but as he tests his luck further, he's more likely to have a bullet connect.
 * This could also be true for his enemies, as it doesn't always take the same number of shots to down a target (even if they're the same type of enemy). If the player can group their shots well so that the target is hit consistently (stunning them with a shot then shooting them again while they're reeling), it only takes about three or four shots (even if none of them are headshots) whereas letting them collect themselves can result in putting six or seven bullets in them before they fall.

Nathan Drake is ex-military.
Nathan is unreasonably good with guns, hand-to-hand combat and keeping his cool in a gunfight for someone who is supposedly 'just' a fortune hunter. Considering his dedication to the treasure hunting trade both for the money and the adventure, it's not unreasonable to assume he enlisted, probably under the Army or Marines, as a grunt, to get physical conditioning for work in the field, build up capital to finance his operations, and to learn how to handle himself in combat, knowing that rival fortune hunters might very well shoot at him before anything else. Notice how he doesn't seem to owe anyone money like Sully, nor does he tire quickly or complain about the lack of amenities while on the job. It would certainly explain his complete, hard-line refusal to  in Among Thieves.

Uncharted 2: Among Thieves is a prequel.
In all of the promotional material that's been released so far, Nathan is not wearing Sir Francis Drake's ring as a necklace. Since the necklace was returned to him at the end of the first game, and since Sir Francis Drake was revealed to be a hero for dying to protect the secret of the island from getting out, you would think that Nathan would continue wearing the necklace as symbol of pride. If, however, Among Thieves is a prequel, it is very possible that Nathan isn't wearing the ring because he hasn't found it yet, and at some point during the game he will acquire it, realize what the numbers written on the ring mean, and decide to check it out, setting into motion the events of the first game. In this case, it would go without saying that the expedition of Among Thieves is going to be a financial bust, because this would explain why Nathan is bothering to chase after treasures "after" the expedition to the island, why he and Sully were hoping that the treasure of the first game was finally the real deal, and why Sully and Elena are not in Among Thieves (not that we know for sure that they aren't, but Naughty Dog hasn't confirmed that they are, and there is a new female love interest, so at this point I'm assuming they're not in).
 * Nope. Not a prequel. Got the interviews to prove it.
 * Elena's role in the trailer also pretty much confirms that this is not a prequel.
 * Interestingly, in the final game, he is still wearing the ring. Maybe Naughty Dog removed it from the trailers to throw us off.
 * This Troper thought it was probably a prequel until he turned the corner to find Elena, mostly because he confused the Panamanian jail referenced in the first game with the Turkish prison.

Nathan Drake hooked up with Eddy Raja's sister.

 * A prequel motion comic has been announced, and will feature a new female character named Rika. Nathan Drake's journal has a page where there are the names and contact info of several women (along with a pressed flower), including Chloe, Elena...and a woman named Rika. The game credits list a voice actor for a currently unknown multiplayer character (probably in future DLC) named Rika Raja. If she is a relation of Eddy's, it would partially explain why Eddy hates Nate so much.
 * Well Drake DID hook up with Rika in the motion comic. However he and Eddy were "bestest pals" before that.
 * So if his relationship with Eddy's sister ended baddly, that would explain why Eddy hates Drake so much.

Nathan Drake is a descendant of Altaïr, and is secretly an Assassin.

 * Think about it, both Altair and Ezio were proficient at parkour and navigating complex obstacles, like Drake. They also had a penchant for getting involved with items with supernatural powers. Plus, Nate and Desmond both share the same voice actor. Nate, in reality, is not a treasure hunter. That's merely a cover so that he can intercept dangerous, supernatural objects before the Templars could get them. El Dorado and the Tree of Life were merely one of the many Pieces of Eden the Templars were looking for. It's even possible that Nate and Desmond are relatives!
 * If Nate is descended from Altair, wouldn't he and Desmond have to be related?
 * I think he means closely related; brothers or first cousins rather than twentieth cousins.
 * Pieces of Eden are high technology left from Those Who Came Before after their civilization was wiped out, and Assassin's Creed 2 establishes that they come in practical forms like staves and swords in addition to the "apples." El Dorado and the Tree of Life don't fit this pattern. Alternatively, El Dorado (or rather, the plague it contains) and the Tree of Life are simply natural holdovers from the way the world was before the solar flare that wiped out Those Who Came Before and nearly wiped out the first of humanity. The Tree of Life could've been what allowed humanity to rise up against their masters in the first place, and some of them couldn't help but overdose on it, becoming the Guardians.
 * Obviously Desmond and Nate are twin brothers.
 * What are you talking about? Nate is clearly Subject 16.
 * That's actually pretty plausible, if you tweak some fine details... Nate was just a somewhat small-time treasure hunter until Abstergo contacted him to help them find Pieces of Eden. Nate went entirely voluntarily, unaware of their cover for the Templars. Because he went of his own free will, they only contacted him every once in a while. After a few sessions in the Animus, they temporarily let him go, and due to the bleeding effect, he became proficient in firearms and parkour. Drake's Fortune happens. Abstergo contacts him again, more sessions in the Animus. This time though, Nate learns a bit of their background, and secretly decides to oppose them, becoming an Assassin. More bleeding effects; this time Nate learns to be stealthy, as well as more climbing. Abstergo, unaware of his opposition, lets him go. Among Thieves happens; Nate opposes Lazarevic because fighting Abstergo taught him about what happens to power in the wrong hands (plus, y'know, for the money). Other stuff happens. Eventually, Abstergo re-captures him and holds him against his will; the bleeding effect comes into full force, and he goes insane. Assassin's Creed happens.
 * "Other stuff happens" Other stuff like Drake following the archaeological work of T.E. Lawrence. (who may or may not be an Assassin/Templar) Finding Masyaf as it is being searched by the Templars, going through a Desmond-y hallucination sequence ultimately culminating in him pulling off an eagle drop only to be re-captured by Abstergo.
 * Bingo. Maybe the guys trying to stop Nate in Uncharted 3 are the Templars!

Uncharted 3's antagonists have Early Bird Cameos in Uncharted 2's updated multiplayer.

 * Recently, Uncharted 2's multiplayer mode was patched so that the level cap was rasied to 80. With this were given two rewards for reaching levels 70 and 80 -- two villain skins called Dutch and Blain. They aren't joke skins like Doughnut Drake or Skelzor and they don't seem to be based on any existing character in the franchise, so there's so far no obvious explanation for where they came from and why they're the rewards for the players that have played the most. Unless they aren't important now, but will be later -- possibly as the next game's main villains.
 * Nope those are just generic enemies from the first game.

Victor Sullivan is both Tom from 500 Days of Summer and Arthur from Inception

 * On the 500 Days of Summer page it's all but confirmed that the narrator of the film is an older Tom Hansen. On the Inception WMG page it's proposed that after breaking up with  Tom changed his name to Arthur and the events of Inception happened. Now the link between all this and Uncharted is the fact that both Victor Sullivan and the narrator in 500 Days of Summer are played by Richard Mc Gonagle. Therefore fun crazy ideas say that after a rich career in dream theft Arthur grew old, changed his name to Victor Sullivan, started engaging in regular theft, eventually met Drake etc.
 * Maybe in between those, he was also Tom Sheldon from Just Cause, using an assumed name because of the undercover nature of his workings with the CIA.

Naughty Dog is Building A World involving Ancient Astronauts who used Organic Technology
The MacGuffin of the first game was a Zombie Plague. The second was a Super Serum. Perhaps they'll even have Drake be part of an ancient warrior bloodline of inherently Badass Normals with Healing Factors.

Drake's Deception will be a big What the Hell, Hero? for Drake
The series gets quite a lot of accusations of Unfortunate Implications and Moral Dissonance on Drake's part. Naughty Dog would probably take the moment to have the villains and other characters call Drake out on his One-Man Army tendencies (and unlike Lazarevic make it look more than just the villain trying to psyche him out).
 * Dropped. No one calls him out on anything.

The
Maybe They're just some of Roman's men who got drunk and

Uncharted 3 will have some sort of Eldritch Abomination or Eldritch Location
The previous two installments have been somewhat Lovecraftian. What with lost cities and unexplained evils. It would make sense that the third game continues with this tradition.
 * Not a particularly wild WMG, since there's a precedent and all, but.

Shambhala wasn't originally in Asia.
It was in Africa, back when it was known as Gondwana. It floated over to Asia along with the rest of India and got stuck in the mountains.

Talbot from Drake's Deception is
Carried over from the Headscratchers page. It's one explanation for his interest in finding Ubar, his use of and his apparent ability to  in Syria. Further implications:

The player is not Nate, but actually a screenwriter for a fictional adventure film series called Uncharted.
Seeing how cinematic the games are, you are not controlling Nate Drake himself, you are writing the action scenes of the Uncharted films while your fellow screenwriter writes the story and plot elements in the cutscenes. The game itself is actually all just in yours and your fellow screenwriter's imagination.
 * And whenever you die, it's the screenwriter crumpling up his paper and saying "Nah, that sucks, let's try that again"? That's actually kind of interesting to think about.

Uncharted IV will take be set in space.
Thirty years have passed since Uncharted 3, during which mankind has made some very rapid technological progress. The protagonist will be the protege of an older Drake, who will have taken over Sully's role. The story will follow exactly the same formula as the first three games, only this time the heroes are looking for a ruined alien city.

Uncharted IV will involve Kid Drake.

 * C'mon! Who would pass up for adventures as Nathan Drake when he was a kid? It'd be like the TV show featuring young Indiana Jones! Or that movie featuring young Sherlock Holmes. The series is just screaming for it, and, from what we see of Kid Drake, he's got the skills. It could be set a few months after he first met Sully in the flashback we see in Uncharted III.

Drake is a young Monkey Fist.

 * Both explorers and he's obviously some sort of monkey. Eventually he'll go to collect the monkey statues and then MONKEY!

Talbot is (or claims to be) a descendant of Edward Talbot, AKA Edward Kelley, the medium who helped John Dee in his work

 * This would complete the Dark!Drake parallel and give some depth to the character.