Biofuels are a bit like hydrogen at this time, they use more energy to produce them, but are cleaner and there's a lot of room for improvement in the efficiency of their production. More research and development will improve the process, but I think biofuels are a holdover, whereas hydrogen has the potential to be a really clean future fuel, although far from perfect, especially as it stands.

2001 Prius Photos       2005 Prius Photos
'97 Prius Simulation Prius inner workings