We consider several approaches to control morphology of self-organized quantum dot (QD) nanostructures. (i) We study effects of temperature and of temperature ramping on formation of QD arrays. The theory of equilibrium distribution of island volumes is developed predicting an entropy-driven decrease of island volume at higher temperatures. Experiments on InAs/GaAs(001) obtained both at submonolayer deposition and in Stranski-Krastanow (SK) growth mode reveal the decrease of island volume with temperature increase that agrees with the thermodynamic picture of island formation. (ii) We show a reversibility of temperature-driven changes in island volume, shape, and density for SK InAs/GaAs(001) islands and a new possibility to control QDs. (iii) We consider an advanced way of formation of complex QD structures. For multisheet arrays of strained islands a transition between correlation and anticorrelation driven by the spacer thickness is predicted theoretically and confirmed experimentally. (iv) The overgrowth of InAs/GaAs islands by an InGa(Al)As alloy leads to alloy phase separation in the capping layer and an effective increase of both the lateral size and the height of the QDs. These complex growth approaches enable us to tune efficiently electronic spectra of the QD systems.