Improvement of fuel cell systems with respect to reliability and efficiency is the main issue in preparing them for their commercialization. Stationary, automotive or portable systems are still at the development stage and a lot of tasks have to be solved as to increase the component and system efficiencies by facilitating the system construction or eliminating parasitic components. To accelerate the development and to determine the systems efficiencies as well as the inaccessible system values, effective standardized tests have to be established and linked with a flexible modeling and simulation environment. A modular model-aided system analysis and development environment is presented which has been evaluated and validated at the IWE. The tool has been applied to a complex prototype stationary PEMFC system, a commercial methanol based PEMFC auxiliary power unit and a fictive stationary SOFC system proving the tool flexibility, modularity and accuracy for a wide range of applications.