Fuel cells (FCs) are important for building combined energy systems due to their high efficiency. Molten Carbonate FCs (MCFC) and Solid Oxide FCs (SOFC) have been identified as best candidates for FC Combined Cycles (FCCC). This paper presents a procedure for evaluating the trends in emission levels and economics of FCCC based energy conversion systems, utilising biomass and/or fossil fuels. This involves significant combinatorial complexity, efficiently handled by the P-graph algorithms. A procedure for the synthesis of cost-optimal FCCC configurations is developed, accounting for the carbon footprint of the technology and fuel options. The results show that such systems employing renewables can be viable for wide range of economic conditions, due to the high energy efficiency of the FC-based systems.