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.
