If there is one thing I would say about Lost it is that they don't believe in coincidences. Everything seems to be carefully plotted and planted...well, mostly everything. The writers and producers are people after all and thus not infallible.
Okay, now that I've gotten completely off subject....
I do not think that it is coincidence that both Locke and Ben have mothers named Emily. How abso-freakin'-perfect would it be if they were half-brothers?
It makes sense. Locke is older than Ben. Emily gets pregnant while seeing someone (at this point we're supposed to believe that it's the original Sawyer, though I have my doubts on that one). Then she gives the baby up for adoption. Later she meets and marries good ol' Roger. After all, her judgment is already proven to be not that great. Emily gets pregnant with Ben and then dies in childbirth.
I know, I know... You're thinking, but we met John's mother. She was in the crazy bin and led him to his father.
But was that actually his mother? Surely it's possible that Anthony Cooper (aka Tom Sawyer aka jerk) hired a woman to play John's mother to reel him in so he could steal his kidney. And that brings me to my other point.
Is Anthony Cooper really John's father? He was a wealthy man who manipulated people for a living. He says something to John that continues to nag at me... "You needed a father figure and I needed a kidney". I would think it would be fairly easy for him to find a lonely man with the same blood type or whatever (I'm not a doctor :) that he could play one more long con on. Why do we ever take anything this show gives us at face value.
However, if Anthony isn't John's father, then the big question is... who is? Someone we know? what other connections could there be with John and the Island - because he's obviously very special.
(On a lighter note... Maybe his father is Richard :D He doesn't age and he would look too old for Emily, even in the 50's and can't you totally see him in a black leather jacket with his hair all slicked back.... hahahaha)