A fuel cell system includes multiple fuel cells. Each fuel cell may be a proton exchange membrane fuel cell that is arranged to optimize the performance of the fuel cell. The fuel cells may include silicon wafer substrates that define flow channels through the fuel cells for hydrogen and oxidant gases. The fuel cells can include obstructions within the flow channels that divert the flow of gases as the gases pass through the fuel cells. The fuel cell system may include multiple fuel cell modules, with each module including multiple stacked fuel cells.