Firstly, this was previously mentioned but being such a new technology means they are still expensive, and more needs to happen in their commercial development before costs can become really competitive because price would have to fall by a factor of 10 for fuel cells to become economically viable (http://www.columbia.edu/~ajs120/hydrogen/web-pages/h-fuel-cell-disadv.html .Although this high price can be because the little experience and research on this sector just as the first computers or mobile phones.
In addition, hydrogen needs to be made. We can't just get hydrogen from the ground like oil, gas, or coal. We need to use energy to make the hydrogen. Because of this hydrogen is NOT an energy source, but an energy store. http://answers.yahoo.com/question/index?qid=20081211191617AAFOqnG
Moreover, hydrogen has much less volumetric energy density than oil or diesel and this makes storage more difficult. Nowadays, development has made posible to increment its energy denstiy by storing hydrogen at 200-350 bar. However, its energy density is still nearly ten times less than oil's. Other storage methods can be used such as luiquid hydrogen wich requires high energy is needed to mantain it in adecuate temperature (-250ºC) or metal hidride storing, wich is very expensive and pretucs are very heavy and have a svery slow recharge. But as storage systems are more complicated than this we prefer to dedicate a whole entry to them. http://www.fuelcell.no/hydrogen_storage_es.htm
Finally, new lithium batteries are leaving fuel cell behind as they are cheaper, easier to store, and the car industry is already using them far more.For example, emerging thin-film lithium polymer batteries created in labs by Solidcore, Cymbet, NASA Glenn Research Center, Voltaflex, ITN, and others have energy densities up to 900 Wh/L and high-pressure hydrogen gas has an energy volume-density of about 400 watt-hours per liter. http://peakenergy.blogspot.com.es/2005/01/batteries-vs-fuel-cells.html