The pressing environmental and political necessities of modern international society call for a suitable array of contingency solutions to the energy question. One valid alternative to fossil fuels, for example, is the use of alternative or nonconventional fuels, derived from waste or biomass. Combining these resources with fuel cell applications would provide a significant contribution to environmentally friendly and efficient energy use. Through a comprehensive literature survey and the collection of practical case studies and operational experience, an assessment of the potential for coupling with high-temperature fuel cells of three technologies of alternative fuel production—landfill, anaerobic digestion, and gasification—has been attempted. Though landfill is the easiest technology, anaerobic digestion produces superior quality gas and has the benefit of yielding extra fertilizer, in the form of digestate. Gasification is the most demanding of the technologies but is very flexible in its feedstock. Furthermore, using steam as a gasifying agent produces high quality syngas. However, the main issue with all three technologies is the removal of contaminants, in particular, sulfur. The application of high-temperature gas cleanup is demonstrated to bring considerable advantages on system level when gasification of nonconventional fuels is considered. Ultimately, the reforming step is a key aspect for optimal cost-effective integration of these alternative systems. The review provided establishes the key characteristics of alternative fuel conversion by landfill, anaerobic digestion, and gasification, and exposes the major points of attention for their subsequent application in high-temperature fuel cells. Indications of the measures required and the developments in the field of basic research and system integration are given to provide clear paths of activity, which should bring about the wide-scale implementation of a truly promising application of fuel cell systems.