In the first part of this work we discuss possible effects of stochastic space-time foam configurations of quantum gravity on the propagation of "flavoured" (Klein-Gordon and Dirac ) neutral particles, such as neutral mesons and neutrinos. The formalism is not the usually assumed Lindblad one, but it is based on random averages of quantum fluctuations of space time metrics over which the propagation of the matter particles is considered. We arrive at expressions for the respective oscillation probabilities between flavours which are quite distinct from the ones pertaining to Lindblad-type decoherence, including in addition to the (expected) Gaussian decay with time, a modification to oscillation behaviour, as well as a power-law cutoff of the time-profile of the respective probability. In the second part we consider space-time foam configurations of quantumfluctuating charged black holes as a way of generating (parts of) neutrino mass differences, mimicking appropriately the celebrated MSW effects of neutrinos in stochastically fluctuating random media. We pay particular attention to disentangling genuine quantum-gravity effects from ordinary effects due to the propagation of a neutrino through ordinary matter. Our results are of interest to precision tests of quantum gravity models using neutrinos as probes.