This isn't the first time I've written on the subject, but since I just started my own blog, I'll recapitulate.
Current proposals for "clean" energy, or energy from non-fossil sources, center around bio-fuels, and hydrogen. IMO, sodium fuel cells are a much better idea, as discussed.
One option for hydrogen, and the main one for bio-fuels, is to use them in internal combustion engines similar to what we use (mostly) today. In addition to the inescapable pollution (nitrogen oxides and/or unburned hydrocarbons), there is the question of energy efficiency: heat engines are limited by Carnot efficiency. They also employ a number of moving parts transferring mechanical energy with associated frictional losses.
Fuel cells avoid this problem, by converting the energy of oxidation directly to electricity, without going through the losses of the Carnot cycle. However, bio-fuels, even used in fuel cells, must be renewed through agriculture. Hydrogen can be produced directly from electricity through electrolysis, which is why so many people focus on it as "ideal" for clean vehicular (and other mobile) energy.
However, hydrogen is very dangerous, and hard to contain. As a liquid, it requires extremely cold temperatures to avoid explosive escape, which in turn requires on-going energy to power the refrigeration. If stored in pressurized form, the energy density is very low, requiring a lot of space to store a little energy. Either way, transferring fuel from a service station to the vehicle would require very sophisticated technology to be safe. Finally, while a service station might be able to create hydrogen directly from water (through electrolysis), it is unlikely that the necessary equipment could be installed in each vehicle, meaning the the option of simply plugging in overnight would not be available.
In contrast, sodium works as well in fuel cells as hydrogen, if not better. It requires a temperature somewhat above that of boiling water to remain liquid, but if the available energy stops it simply solidifies. When oxidized, it produces sodium oxide, a solid chemical that is caustic, but fairly easy to handle. In order to recharge by electrolyzing it, an appropriate solvent would have to be developed, but that is probably feasible. When calling at a service station, the sodium oxide would be traded for an equivalent amount of (liquid) elemental sodium (with some payment). The facilities for recharging could also probably be built directly into the vehicle,, allowing plug-inn overnight.