It comes out as CO2 - something that gets downplayed of course. The greenies just can't seem to win - their beloved fuel cells produce "global warming" gases, windmills are an eyesore and kill birds, hydro dams up rivers... There just isn't any free lunch.
Here's a great reference on the direct methanol fuel cell chemical reaction.
That Link is a great reference.
I didn't know there were so many different types of Fuel Cells.