Tom Clancy's Splinter Cell/WMG

Sam Fisher is a Reader.
Compare Mark and Execute to how River kills the goons at the end of "War Stories." They're almost exactly the same thing - quickly locating the positions of targets to be killed, and then gunning them down all at once in a flurry of hyper-accurate gunfire. Thus, either Sam is a low-level psychic who likely doesn't know of his abilities, or he has something similar to River's savant-level skill with firearms and mathematics.

Every time Sam dies in gameplay, he was just planning how to deal with the enemies.
Sam Fisher is such a badass that this has to be true!
 * Alternatively, he is simply recounting tales of his previous missions to new Splinter Cells (pre Conviction of course) and he simply has the same story telling abilities as the Prince from The Sands of Time.

Sam's Charles Atlas Superpowers will eventually include being able to truly turn out all the lights.
In some missions you cannot eliminate all the light sources even if all the artificial lighting is of the breakable sort. Why? You can usually blame the moon and sun. As his Charles Atlas Superpower grows past the current stage of "merely" keeping track of enemies' movements even without line-of-sight, though...

The Meggido are The Templars by another name.
They're a secret, supposedly all-reaching organisation concerned with seizing power and control... in an Ubisoft game. How was this not here before?

The Mark part of Mark & Execute is really an Assassin talent.
Sam isn't descended from Altair/Ezio's bloodline, so he can't use Eagle Vision. However, his ancestors did have the ability to keep track of those they've targetted even after losing LOS. Sometime between Double Agent and Conviction he decided to embrace his heritage and seek training to make use of it properly. If, going with the above WMG, Meggido really is (related) to the Templars, then there may be a crossover where Sam properly throws his lot in with the Assassins. After all, the original idea was for Conviction to use social stealth - possibly using a similar model to AC? I pity the fool...

Megiddo was behind the events of H.A.W.X. 2.
In the final mission, Morganov admits he was convinced to betray his country by "those people" and that nobody can do anything against them, which is why he has no choice but to launch the nukes. Sounds a lot like Tom Reed in Conviction's ending.
 * I guess it is correct. The box art for H.A.W.X. 2 says that it is in the same conflict as Ghost Recon Future Soldier, which would be set in the same conflict as Splinter Cell Conviction.

The lightbulbs are supplied by the lowest bidder
It's easy to say that The Guards Must Be Crazy when YOU shot that lightbulb. But what if we were the 15th, and it was the 4th lightbulb to go off?

Sam has three eyes.
The only people who know about it, besides himself of course, are Lambert, Grim, possibly Sarah, and certain high level members of Third Echelon. Sam's third eye, located on his forehead, has excellent night vision, but is extremely sensative to light, so he has to keep it closed and unnoticed for most of the time. Third Echelon gave him the iconic goggles in order to allow him to keep the eye protected so it could be open and, thus, and make full use of its abilities. In order to not arouse suspicion, they created different versions of the goggles for other Splinter Cells claiming that the third lense was the only way they could fit in both night vision and thermal vision. As a result of using the goggles, Sam has made his extra eye even more perceptive, so much so that it can see through its eyelid, while still being protected from light.
 * What.

"Sam Fisher" is now the Dread Pirate Roberts
Saw this on SB, thought there might be something to it. Like the James Bond theory, "Sam Fisher" has become the code-name for an agent, rather than the man's real name. Looking at the Blacklist trailer, Sam looks a bit younger than he did in Conviction, and (assuming it's not a placeholder), has a newer, younger-sounding voice. The real Sam was tired of the spy game, he was sick of the machinations. It makes sense that once he got his daughter back and freed Victor Coste, he'd retire, permanently this time. But when setting up Fourth Echelon, the powers that be decided that to name the command position after the premiere operative of Third Echelon, and the person who saved the President from their betrayal.