Three-dimensional (3D) technologies enable faster, smaller and more energy efficient systems. Moreover, after more than two decades of research, the technologies are mature and ready for industrial application. However, only few developers make use of them and adoption by market is lagging behind. One of the main reasons is that 3D technologies are difficult to be integrated into existing two-dimensional (2D) design flows, with the latter often wasting the potential promised by 3D technologies. Therefore, 3D-compatible design flows, with an emphasis on co-design between various 3D hierarchy levels, are required. In this paper, we first give an overview of the most relevant and mature 3D technologies. Subsequently, we investigate related design methodologies in order to find so far neglected potentials for design optimiza