Okay so I am sure this is not a new thing to the lost fan base when it comes to theories But I am pretty certain that Desmond's dad Is Jacob.
He is the only important character which we do not know the family history of other then his dad left when he was young. If Jacob is his father it might explain why Desmond is so special and certain rules do not apply to him. This might play as a big story line somewhere in season 6. Desmond has been so under used lately and for him to be so important you know he is gonna do something big soon.
Now the only other thing I can't figure out is who is mom is. I am going with llana for now, only cause Jacob and her seem to have a history , it is clear they know each other by her saying "it's nice to see you again". Seems reasonable to me. Any other suggestions.
This is my first post by the way.