There is a phenomenon that is fairly well documented and known among high-altitude mountain climbers, in which climbers high on the mountain develop a strong sense that they have a companion with them. They don't see anyone when they look around--it's not a visual hallucination--they just sort of know that there is another person there with them. The only reference I can think of off the top of my head is Greg Child, who wrote about it in his book "Mixed Emotions."
This sounds a lot like the theory that humans used to have more separate brain hemispheres (pre- corpus colossum), and thus had a higher prevalence of schizophrenia (messages from the right side of the brain to the left, perceived as coming from "outside the self") which was interpreted as a voice of God.
Whoops. After reading my own link, I saw that the god helmet experiments have yet to be recreated. I had heard about it in a Dawkins Documentary and assumed that the science behind it was more solid than it actually is. My apologies for bringing hokeyness to this conversation.
I tend to wonder if our minds have a connection to Earth's magnetic field, perhaps using it as a sort of external hardrive at times, but if that was the case I wonder why the lunar astronauts didn't (literally) lose their minds.
One of the God Helmet scientists (Michael Persinger) hinted at that in one of his lectures I saw, a coincidental synchronicity with the planet's magnetic field, almost akin to the saltiness of our blood being the same as the oceans.