The output power of a free electron laser (FEL) has extremely high variance even when all FEL parameter set points are held constant because of the stochastic nature of the self-amplified spontaneous emission (SASE) FEL process, drift of thousands of coupled parameters, such as thermal drifts, and uncertainty and time variation of the electron distribution coming off of the photo cathode and entering the accelerator. In this work, we demonstrate the application of automatic, model-independent feedback for the maximization of average pulse energy of the light produced by free electron lasers. We present experimental results from both the European x-ray free electron laser at DESY and from the Linac Coherent Light Source at SLAC. We demonstrate application of the technique on rf systems for automatically adjusting the longitudinal phase space of the beam, for adjusting the phase shifter gaps between the undulators, and for adjusting steering magnets between undulator sections to maximize the FEL output power. We show that we can tune up to 105 components simultaneously based only on noisy average bunch energy measurements.