Atomistic strain simulations based on the valence force field method are employed to study the vertical arrangements of semiconductor quantum dot (QD) multilayers. The effects of the QD shape, dimensions, and materials parameters are systematically investigated, varying independently the following parameters: spacer width H, QD lateral spacing D, base b, and height h, slope of the side facets, elastic properties of the dot and the substrate materials, and lattice mismatch between the dot and the substrate. The transition between vertically aligned and anti-aligned structures is found to be determined mainly by the ratios H/D and b/D, as well as by the strain anisotropy of the substrate and to a lesser extent of the QD. The dependence on the QD height h is significant only for steep side facets and large aspect ratios h/b, and the effects of the lattice mismatch strain and the bulk elastic moduli are found to be negligible. The comparison with experimental data shows an excellent agreement with the results from the simulations, demonstrating that the presented analysis results in precise theoretical predictions for the vertical self-organization regime in a wide range of QD materials systems.