We provide an overview of a novel self-assembly process that occurrs during GeSi/Si(001) strain-layer heteroepitaxy under conditions of limited adatom mobility. Suppression of copious surface diffusion leads to limited three-dimensional roughening in the form of pits that partially consume a thick, metastable wetting layer. The material ejected from the pits accumulates alongside, eventually forming a symmetric quantum dot molecule consisting of four islands bound to a {105}-faceted pit. These structures, which are of interest in nanologic applications, appear to arise from an intrinsic strain-relief mechanism in a relatively narrow regime of deposition conditions. An additional degree of morphological control is obtained by annealing films containing pits, before they evolve to full quantum dot molecules. Annealing promotes a one-dimensional growth instability leading to the formation of highly anisotropic grooves, bounded by long, wire-like islands. Finally, we show that patterns created in the Si substrate using a focused ion beam can control the location of quantum dot molecules, which is an additional critical step towards being able to use these structures for computing.