Mine howls all night long!
You are not alone, there are many posts on various forums reporting the same noises from GE side-by-sides.
Mine produces an incrediby annoying howl for hours at a time. It sounds like it is caused by airflow, almost like blowing into a bottle (only much louder).
Some have suggested that replacing the evaporator motor, located in the freezer at the bottom, behind the panel. This would seem to make sense, and the original post remined me that I did not notice the noise being present when the unit was new (2-3 years). If it were airflow across some sort of part in the evaporator area, I would expect it to make the noice any time the fan is blowing.
I do recall awaking to a slightly ajar freezer door one morning. This required me to empty the freezer and dry everything out. To be sure I had all of the water cleaned up, I went ahead and removed the ice maker, and the panels in the back of the freezer. I recall the noise was being made even with the panel removed, and therefore no significant air movement at all.
I think the fan motor may actually be the cause. Someone correct me if I am wrong, but these fans operate at variable speeds, which would explain the intermittent nature of the noise. The only thing I can imagine is wind noise caused by some sort of damper.
I hate to spend $60 on a new fan motor in vain, but the noise is so loud and annoying its either a going to fix it, or it I am going to take a sledge hammer to it!
For the original poster - take care of it now, because it gets much worse (louder and longer) over time!