In this review article several aspects of four-dimensional, non-perturbative N = 1 compactifications of string theory are analysed. he focus lies on brane dynamics and their effective physics as encoded in the holomorphic couplings of the low-energy N = 1 effective action, most prominently the superpotential W. In the first part of the article the effective action of a spacetime-filling D5-brane in generic Type IIB Calabi-Yau orientifold compactifications is presented. In the second part the author invokes tools from string dualities namely from F-theory, heterotic/F-theory duality and mirror symmetry, for a more elaborate study of the dynamics of (p, q) 7-branes and heterotic five-branes. Exact computations of the complete perturbative effective superpotential, both due to branes and background fluxes are performed. Finally, in the third part the author presents a novel geometric description of fivebranes in Type IIB and heterotic M-theory Calabi-Yau compactifications via a non-Calabi-Yau threefold that is canonically constructed from the original five-brane and the Calabi-Yau threefold via a blow-up. The blow-up threefold is used to derive open-closed Picard-Fuchs differential equations, that govern the complete effective brane and flux superpotential. In addition, first evidence of a consistent interpretion of as a flux compactification geometrically dual to the original five-brane is presented.