In Stranski-Krastanov growth of SiGe films on Si(001) a series of stress-induced morphologies occurs including step-bunching of the pre-existing substrate steps and formation of faceted three-dimensional islands. We demonstrate how one can utilize these elastic strain-relief mechanisms to create a variety of large-scale arrays of uniform nanostructures simply by growing under appropriate conditions of substrate vicinality and misfit. By tuning substrate miscut periodic ripple structures down to a few ten nm are obtained. Self-organized growth of faceted islands can be achieved either by stress-induced self-organization in SiGe/Si multilayer films or in a single alloy film by combining step bunching and island formation mechanisms. We expect these concepts to become useful for the fabrication of large-scale arrays that may serve, for example, as quantum wire and quantum dot arrays or act as patterned substrates for deposition of various materials.