It's pretty obvious what really happened.....they were beamed aboard an alien spacecraft where they underwent medical experiments. One of those included the labotomy so they forgot where they had come from. Easy when you put your mind to it :p

http://planetsmilies.net/alien-smiley-126.gif

I always believed that the ship that supposedly "found" the Mary Celeste were the ones responsible for the crew being missing. Just a simple act of Piracy and Murder in order to claim salvage rights over the cargo and ship. In fact,I remember reading that during the initial investigation that they considered trying the captain and crew of the other ship with piracy,but didn't have the evidence to back it up.

From what I understood, it was generally believed to be an insurance fraud in most circles. Why not just sink the boat, that's beyond my comprehension.