Also from the UNH Biodiesel Group, a very helpful comparison of fuels, comparing gasoline, petroleum diesel, biodiesel, H2 fuel cell, and both diesel and gasoline hybrids. The fuel pricing is clearly a little out of date (less than $2.00 per gallon of gasoline.) (Click to enlarge.)
The referenced link in footnote 6 explains the concept of fossil fuel energy balance and life cycle inventory -- essentially, are you net gaining or losing energy once all factors are taken into consideration. Of the fuels compared, biodiesel comes out on top.
The prototype diesel hybrid running biodiesel does very well.