  We study different aspects of the non-perturbative superpotentials induced by
Euclidean E3-branes on systems of D3/D7-branes located at Abelian orbifold
singularities. We discuss in detail how the induced couplings are consistent
with the U(1) symmetries carried by the D3/D7-branes. We construct different
compact and non-compact examples, and show phenomenologically relevant
couplings like $\mu$-terms or certain Yukawa couplings generated by these E3
instantons. Some other novel effects are described. We show an example where
E3-instantons combine with standard gauge instantons to yield new
multi-instanton effects contributing to superpotential, along the lines of
ref.\cite{geu}. In the case of non-SUSY $Z_N$ tachyon-free singularities it is
shown how E3-instantons give rise to non perturbative scalar couplings
including exponentially suppressed scalar bilinears.
