A wide range of bioenergy crops has been proposed as feedstocks that can serve as renewable and ecologically sound substitutes to fossil fuels. In the United States, corn grain (Zea mays) ethanol is the primary biofuel, with over 49 billion liters produced in 2010. Along with the Energy Independence and Security Act (EISA) of 2007 mandate, concerns about competition for food, land availability, nutrient and water requirements, energy balances, and greenhouse gas (GHG) emissions have prompted researchers to investigate other potential feedstocks. These include second-generation lignocellulosic feedstock and third-generation biodiesel from microalgae and cyanobacteria. However, each feedstock option has associated benefits and consequences for its use. One technique used to evaluate the energy efficiency of bioenergy production systems is the life-cycle assessment (LCA), where system inputs and outputs are computed in terms of either C or energy equivalents to assess the net gains in energy or C offsets. This article collates and synthesizes information about feedstock production options. Results show a wide range of calculated energy and GHG balances, even for the same feedstock species. Discrepancies in LCA and uncertainty thus make direct comparisons difficult and prevent a consensus in determining feedstock suitability. Recommendations must be based upon LCA model assumptions, crop species, cultivation methods, management practices, and energy conversion choices. Currently lignocellulosic feedstock, while a better alternative than corn grain, is not a long-term viable energy source. New feedstocks and technologies are necessary if bioenergy is to be C-neutral and efficient in energy production and land use. Although C fluxes are considered in LCA, one important ecosystem C stock that has previously been left out of many LCA models is changes to soil organic carbon (SOC). Future research, developments, and priorities are discussed for options to produce low C fuel sources and stabilize the climate.