41 pages, 2 figures.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 μ-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.[28]. 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.This work has been supported by the European Commission under RTN European Programs MRTN-CT-2004-503369, MRTN-CT-2004-005105, by the CICYT (Spain), the Comunidad de Madrid under project HEPHACOS P-ESP-00346 and the Ingenio 2010 CONSOLIDER program CPAN.