Concerns over the economics, supply chain, and emissions of greenhouse gases associated with the wide use of fossil fuels have led to increasing interest in developing alternative and renewable fuels for stationary power generation and transportation systems. Although there is considerable uncertainty regarding the economic and environmental impacts of alternative and renewable fuels, there is a great need for assessment of potential and emerging fuels to guide research priorities and infrastructure investment. Likewise, there is a great need to identify potential unintended adverse impacts of new fuels and related power systems before they are widely adopted. Historically, the environmental impacts of emerging fuels and power systems have largely focused on carbon dioxide emissions, often called the carbon footprint, which is used to assess impacts on climate change. Such assessments largely ignore the large impacts of emissions of other air pollutants. Given the potential changes in emissions of air pollutants associated with the large-scale use of new and emerging fuels and power systems, there is a great need to better guide efforts to develop new fuels and power systems that can avoid unexpected adverse impacts on the environment and human health. This review covers the nature of emissions, including the key components and impacts from the use of fuels, and the design criteria for future fuels and associated power systems to assure that the non-CO2 adverse impacts of stationary power generation and transportation are minimized.