It could be separation anxiety, or a bit of a fear of the dark. Some children, even young babies, go through periods of fear, especially at night. Have you tried a night light? My daughter (now 15 yrs old) did this, I would play a soft, lullaby tape that i had. Maybe you could find a lullaby CD and start playing it before you put him in the crib. Sometimes you just have to let them cry it out too, just go in and check on him every 10 minutes or so to reassure him that you are there, but don't pick him up or stay in the room very long, only a few seconds.
anyway, hope this helps!