Hancock/WMG

Hancock is Horus
Given the repeated imagery of Eagles, that he's possibly thousands of years old and was once part of a people that were considered "Gods"... he may have originally been Horus.
 * The name Horus' actually has both the meaning "One who is above" and "The distant one", which both describe Hancock's personality rather well.

Hancock and the other immortals are the result of yet another Goa'uld attempt to create the perfect host during their rule over Earth.
It worked too well. The immortals rebelled against their creators and, with the aid of the native human populace, forced them to retreat. Then they took up the roles that the Goa'uld had held, ruling entire kingdoms as physical gods until they found their destined partners and became mortal.

Hancock is Jesus.
Literally. The name "Mary" is not a coincidence. He was crucified (more precisely, was crucifiable) because he and Mary were together at the time.

She does specifically tell him that his purpose on earth is to save humanity.

Hancock is Neville.
He started to develop powers without noticing and survived the explosion with only some scratches and amnesia. He's in the repopulated world, which would mean that he's probably not aging. Any location changes, year inconsistencies, etc. come from people rescuing him and taking the man somewhere else, and changing their calendar. He's probably really over 2000 years old.
 * Mary says they've gotten engaged and broken up every century since 3000 B.C. Definitely over 2000 years old.

Hancock and Mary have a child.
Mary met Ray when he was shopping for diapers. Ray, being a clueless new father, needed help choosing between brands. According to Ray, Mary helped him out and eventually they formed a relationship. It's possible that Mary was able to help Ray because she'd had a child of her own. She and Hancock had been together for millenia, and effective birth control hasn't existed all that long. Assuming they're capable of reproducing, it'd be fairly surprising if they didn't have a child. This could go one of two ways:
 * The child is immortal. It would be an adult by the time the movie takes place, and likely off on it's own somewhere. Mary didn't mention it because a)she just never had a chance to bring it up, or b)their child has been off having his/her own adventures for so long that it's all but forgotten.
 * The child is mortal. If the child were conceived and born when Hancock and Mary were sticking together, and thus mortal, the child is probably mortal as well. Once Mary and Hancock split, Mary regains her powers, but since the child was born mortal his/her powers never manifest. Mary had to give up her child so that it could live a happy mortal life.
 * Actually, in ancient egypt they had a birth control so effective they farmed it to extinction. Birth control is Older Than Print.

Hancock is a Time Lo-THONK!!!
We apologize for the previous WMG, the troper responsible has been restrained and sedated.

Hancock really .
Look closely, and you will realize that he is out. Whoever created them decided that he was still needed, so they sent him back.

Hancock and Mary's Son was Dr. Josef Heister.
Think about it, Hancock has a really weird fetish of sticking people's heads up asses and this later went on to Dr. Josef Heister and this is how he actually wants to create a Human Centipede because he saw his pa create millions of them over the years. But he later died because both his mom and father actually met each other before.

The french kid is really Michael Myers.
Their played by the same actor, the kids name is Michel (Pronounced Mee Shell) and they both start out as Jerks.