“The emerging bioeconomy is likely to result in the single largest reconfiguration of the agricultural landscape since the advent of industrial agriculture. This change includes a large-scale shift toward perennial plants, increased appropriation of net primary production for biomass relative to food, and intensification of crop production on marginal, previously fallowed lands” [71]. In most of the developed world, the current system of agriculture has grown over the last 150 years with accelerating changes for the last 65-70 years. The biofuels revolution in agriculture and forestry could be largely complete in 10-15% of that time (2005-2022) if RFS2 goals are met. Even with delays in meeting these goals, which now seem inevitable, changes are likely to be largely completed in 25-30 years. To both assure that mandated sustainability goals are met and that bioenergy resources are available into the future, new knowledge and new tools are needed to evaluate the sustainability of this revolutionary change in the modern societal role of agriculture and forestry. The most appropriate means to analyze options for sustainability of the bioenergy based economy is to focus on net energy from a combined feedstock production/conversion technology and to determine the environmental costs per unit of net energy [35]. Minimizing the environmental cost per unit of net energy will help meet both short and long-term economic and environmental goals for bioenergy. It is likely that investments and policy decisions that do not seek to minimize the environmental cost per unit of net energy will decrease the long-term sustainability of bioenergy. Although in the short run other policy and technical considerations may drive investments in less sustainable directions, “footprint” evaluations based on net energy from a given final fuel product are needed to establish the right mixes of feedstocks and fuels for every region.