Jeff Vail puts forward a compelling, albeit rather limited in scope, “Energy Theory of Value and the EROI of Alternative Energy“.
The problem with analysis like this, as one of his commentators pointed out, is that it does not account for the larger impact of shifting to alternative methods of producing energy, let alone new sources. In other words, if you can fuel your conversion system with waste or by-products then you are essentially performing a clean-up operation. Ethanol has this capability, as does bio-diesel. In fact, bio-diesel could be seen primarily as a recyling process that generates a new fuel source from extant waste.
I also must make the point that new forms of energy may involve significantly more efficient engines and technology that is less centralized and therefore more resiliant. Diesel is known to run longer and require less maintenance than gasoline, so the total energy formula can actually show that alternative energies have a higher ROI, as Rudolf Diesel himself predicted.