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In this paper we present a comparative study of the agglomeration process in silicon-on-insulator (SOI), silicon germanium-om-insulator (SGOI), and strained SOI (SSOI) thin layers under thermal annealing in ultrahigh vacuum. In particular, we provide the first evidence and characterization of agglomeration in SGOI and SSOI substrates. A common agglomeration dynamics is observed in all the substrates investigated, with the semiconductor-on-insulator layer thickness being the main parameter governing it. These findings provide a better understanding of the surface-energy-driven dewetting phenomenon in semiconductor layers and allow us to single out the influence of the surface and stress energies on the void formation and evolution, as well as on the size and density of the agglomerated islands.