This research explores the thermodynamics, economics, and environmental impacts of innovative, stationary, polygenerative fuel cell systems (FCSs). Each main report section is split into four subsections. The first subsection, 'Potential Greenhouse Gas (GHG) Impact of Stationary FCSs,' quantifies the degree to which GHG emissions can be reduced at a U.S. regional level with the implementation of different FCS designs. The second subsection, 'Optimizing the Design of Combined Heat and Power (CHP) FCSs,' discusses energy network optimization models that evaluate novel strategies for operating CHP FCSs so as to minimize (1) electricity and heating costs for building owners and (2) emissions of the primary GHG - carbon dioxide (CO{sub 2}). The third subsection, 'Optimizing the Design of Combined Cooling, Heating, and Electric Power (CCHP) FCSs,' is similar to the second subsection but is expanded to include capturing FCS heat with absorptive cooling cycles to produce cooling energy. The fourth subsection, - Thermodynamic and Chemical Engineering Models of CCHP FCSs,' discusses the physics and thermodynamic limits of CCHP FCSs.