The strain driven self-assembly of faceted Ge nanocrystals during epitaxy on Si(001) to form quantum dots (QDs) is by now well known. We have also recently provided an understanding of the thermodynamic driving force for directed assembly of QDs on bulk Si (extendable to other QD systems) based on local chemical potential and curvature of the surface. Silicon-on-insulator (SOI) produces unique new phenomena. The essential thermodynamic instability of the very thin crystalline layer (called the template layer) resting on an oxide can cause this layer, under appropriate conditions, to dewet, agglomerate, and self-organize into an array of Si nanocrystals. Using low-energy electron microscopy (LEEM), we observe this process and, with the help of first-principles total-energy calculations, we provide a quantitative understanding of this pattern formation. The Si nanocrystal pattern formation can be controlled by lithographic patterning of the SOI prior to the dewetting process. The resulting patterns of electrically isolated Si nanocrystals can in turn be used as a template for growth of nanostructures, such as carbon nanotubes (CNTs). Finally we show that this growth may be controlled by the flow dynamics of the feed gas across the substrate.