I saw a really good programme about this ship recently. Apparently it was carrying American alcohol (1701 barrels of it to be precise). The programme speculated that a spark may have caused a huge fireball that didn't actually burn anything(because only the fumes would have burnt,and burnt quickly). This may have been enough to scare the crew into getting into a smaller boat attactched to the Mary Celeste by a rope.This was standard practice in the event of an onboard fire. Had they not tied the rope properly in their haste to exit, they may have found themselves adrift with no hope of getting back.
Arthur Conan Doyle wrote a story later and changed the name of the ship to the Marie Celeste and thats where all the spooky stuff was added.
Good website
http://www.maryceleste.net/part2.htm