Boeing’s making a series of firsts in aviation, with the latest being a manned flight powered by fuel cells (though batteries helped the plane take off).  While it’s unlikely they’ll power commercial airliners, they may see usage in secondary power capacities or they “could power small manned and unmanned air vehicles.”

This seems to be a more likely future for fuel cells in aviation.  The main benefits here are lighter weight than batteries (since they’ll consume hydrogen, making the plane lighter) and a chance to keep the combustible fuel far from quickly moving parts like the propeller.