Runtime reconfigurable architectures based on Field-Programmable Gate Arrays (FPGAs) are attractive for realizing complex applications. However, being manufactured in latest semiconductor process technologies, FPGAs are increasingly prone to aging effects, which reduce the reliability of such systems and must be tackled by aging mitigation and application of fault tolerance techniques. This paper presents module diversification, a novel design method that creates different configurations for runtime reconfigurable modules. Our method provides fault tolerance by creating the minimal number of configurations such that for any faulty Configurable Logic Block (CLB) there is at least one configuration that does not use that CLB. Additionally, we determine the fraction of time that each configuration should be used to balance the stress and to mitigate the aging process in FPGA-based runtime reconfigurable systems. The generated configurations significantly improve reliability by fault-tolerance and aging mitigation.