There are certain algae that produce hydrogen as a waste byproduct, and the cultivation of such algae and collection of their hydrogen emissions has so far proven somewhat successful (AE 2009). Continued refinement of this process and a bolstering of its efficiency could lead to commercially and industrially viable production levels. There are also methods for extracting hydrogen from waste materials that makes use at least partially of the natural breakdown of these materials; though energy is used in this decomposition, it is not energy transformed and applied at human expense, eliminating its strain on the system (AE 2009). Complex new storage mechanisms are also making the concept of hydrogen fuel cells in cars more viable (U.S. Dept. Of Energy 2009). There have been several major test projects involving hydrogen-powered vehicles in land, air, and sea, including the use of drone spy planes by the U.S. military, municipality waste removal trucks, and a UPS delivery truck (AE 2009; EPA...

All of these show the great promise that hydrogen fuel cells carry for the future.
Though the issue of hydrogen production remains a major kink in the system, continuing research is constantly improving the efficiency of hydrogen extraction and storage. Once these processes reach a certain level of efficiency, there will be nothing other than politics (and economics) to keep this technology from entering widespread commercial and industrial use. Its by product -- water -- can be directly recycled into the raw material for more fuel, making this highly renewable and totally clean.

References

AE. (2009). "Hydrogen Fuel." Accessed 12 December 2009. http://www.alternative-energy-news.info/technology/hydrogen-fuel/

EPA (2009). "Fuel Cells and Vehicles." Accessed 12 December 2009. http://www.epa.gov/fuelcell/

US. Dept. Of Energy. (2009). "Hydrogen." Accessed 12 December 2009. http://www.fueleconomy.gov/Feg/hydrogen.shtml