Deus Ex/WMG

Deus Ex and Assassin's Creed take place in the same 'verse.
It was stated that the Illuminati had the most power in the 20th century, so perhaps the Templars took over at the start of the 21st? Then the thing with Miles happens, weakening them, allowing them to be mostly stopped wiped out. Then MJ12 rears it's head and takes over.

Alternatively Deus Ex and Metal Gear Solid take place in the same 'verse.
The Illuminati are the successors to the Patriots after they became defunct. The Cyborg Ninja program and GECKO program are the predecessors to the augments that Adam uses, which eventually give way to J.C. Denton's nanomachines once the public begins to trust them again, which they certainly wouldn't after the events of Guns Of The Patriots.
 * This would make Smuggler a relative of Drebin, they even look similar, and Have the same voice actor

JC is a vampire.
This is why he can stand behind a MJ12 trooper who is looking in the mirror and still be unnoticed. That would also mean a vampire can see his own reflection, but the others cannot. It would also explain vampires' facility for the use of hair gel.

JC has passive nightvision.
One thing that always bothered me about Deus Ex is how enemies can see you more/less in plain sight, and still not seem to notice you. Also, in a oft-quoted line, JC says that "my vision is augmented", yet at that point it's impossible to have any of the vision-related augmentations. The logical solution is that JC has a passive visual augmentation - he sees much more clearly than the NPCs, so an area that appears to moderately dark for him (ie most of the game) is actually much darker through the NPC's eyes.
 * This HAS to be true, otherwise everything would appear dark and blurry due to his insistence on permanently wearing his sunglasses. One can only wonder how amazing his eyesight would be if he took them off for once.
 * Also, if you look at JC's sunglasses closely, you can see two blue dots. He wears his sunglasses to conceal his augmented eyes, which would be very visible in the dark.
 * No word on how this works out in brightly lit labs and complexes, or against augmented mooks. Perhaps they just don't have the passive vision aug?

JC hears the background music.
At the first visit to UNATCO Alex mentions the idea to plug JC into an online Jukebox. Probably that's a relief for him, since there seems to be no effective firewall for Infolink, so everybody and his dog try to chat with him, what probably would annoy anybody after some time.

JC was augmented so that chain-eating candy bars would heal his injuries.
He has some kind of augmentation that, after allowing the body to take in a set number of calories for the day (calculated considering JC's size and weight and how much he must burn running around killing people), any extraneous calories that JC consumes are used as energy to fuel some rudimentary regeneration and healing capabilities. It still takes some energy to process the food, especially junk like candy, soda, and booze, so the output is not extreme. It would explain, at least, why his body processes alcohol into hit points so quickly with only a few minutes of drunkenness, because there's an artificial structure in place to make that happen with far more efficiency than regular old organs. (Yes, I've been playing video games for years and it still bothers me when I eat ten candy bars and suddenly my leg isn't broken anymore.)
 * The manual actually states that "the nano-systems in your body can take complex carbohydrates and use them as 'fuel' to repair physical damage" and that "alcoholic beverages also do limited healing, but your nano-metabolism accelerates their intoxicating effects. Expect to experience a few moments of disorientation after metabolizing alcohol".