  We perform a systematic analysis of globally consistent D-brane quivers which
realize the MSSM, and analyze them with respect to their Yukawa couplings.
Often, desired couplings are perturbatively forbidden due to the presence of
global U(1) symmetries. We investigate the conditions under which D-brane
instantons will induce these missing couplings without generating other
phenomenological drawbacks, such as R-parity violating couplings or a mu-term
which is too large. Furthermore, we systematically analyze which quivers allow
for a mechanism that can account for the small neutrino masses and other
experimentally observed hierarchies. We show that only a small fraction of the
globally consistent D-brane quivers exhibits phenomenology compatible with
experimental observations.
