  We study the effects produced by D-brane instantons on the holomorphic
quantities of a D-brane gauge theory at an orbifold singularity. These effects
are not limited to reproducing the well known contributions of the gauge theory
instantons but also generate extra terms in the superpotential or the
prepotential. On these brane instantons there are some neutral fermionic
zero-modes in addition to the ones expected from broken supertranslations. They
are crucial in correctly reproducing effects which are dual to gauge theory
instantons, but they may make some other interesting contributions vanish. We
analyze how orientifold projections can remove these zero-modes and thus allow
for new superpotential terms. These terms contribute to the dynamics of the
effective gauge theory, for instance in the stabilization of runaway
directions.
