Two aspects of the topological string and its applications are considered in this thesis. Firstly, non-perturbative contributions to the OSV conjecture relating four-dimensional extremal black holes and the closed topological string partition function are studied. A new technique is formulated for encapsulating these contributions for the case of a Calabi-Yau manifold constructed by fibering two line bundle over a torus, with the unexpected property that the resulting non-perturbative completion of the topological string partition function is such that the black hole partition function is equal to a product of a chiral and an anti-chiral function. This new approach is considered both in the context of the requirement of background independence for the topological string, and for more general Calabi-Yau manifolds. Secondly, this thesis provides a microscopic derivation of the open topological string holomorphic anomaly equations proposed by Walcher in arXiv:0705.4098 under the assumption that open string moduli do not contribute. In doing so, however, new anomalies are found for compact Calabi-Yau manifolds when the disk one-point functions (string to boundary amplitudes) are non-zero. These new anomalies introduce coupling to wrong moduli (complex structure moduli in A-model and Kahler moduli in B-model), and spoil the recursive structure of the holomorphic anomaly equations. For vanishing disk one-point functions, the open string holomorphic anomaly equations can be integrated to solve for amplitudes recursively, using a Feynman diagram approach, for which a proof is presented.