Combined heat and power generation (CHP) is regarded as one of the cornerstones of a future sustainable energy system. The application of this approach can be substantially extended by employing fuel cell technologies in small units for supplying heat to residential buildings. This could create an additional market for combined heat and power generation corresponding to approx. 25% of the final energy demand in Germany today. In parallel, the extensive application of distributed fuel cell systems in residential buildings would have substantial effects on energy infrastructures, primary energy demand, the energy mix and greenhouse gas emissions. It is the aim of the present study to quantify these effects via scenario modelling of energy demand and supply for Germany up to the year 2050. Two scenarios, $\textit{reference}$ and $\textit{ecological commitment}$, are set up, and the application and operation of fuel cell plants in the future stock of residential buildings is simulated by a bottom-up approach. A model of the building stock was developed for this purpose, consisting of 213 types of reference buildings, as well as detailed simulation models of the plant operation modes. The aim was, furthermore, to identify economically and ecologically optimised plant designs and operation modes for fuel cells in residential buildings. Under the assumed conditions of the energy economy, economically optimised plant sizes for typical one- or two-family homes are in the range of a generating capacity of a few hundred watts of electrical power. Plant sizes of 2 to 4.7 kWel as discussed today are only economically feasible in multifamily dwellings. The abolition of the CHP bonus reduces profitability, especially for larger plants operated by contractors. In future, special strategies for power generation and supply can be an economically useful addition for the heat-oriented operation mode of fuel cells. On the basis of the assumed conditions of the energy economy, a technical potential for heat generation by fuel cells ...