The phonon spectrum of self-organised Ge dot superlattices grown by molecular beam epitaxy (MBE) of Ge and Si layers utilising Stranski-Krastanov growth mode was studied by Raman scattering using macro- and micro-Raman experimental setup. The strain and interdiffusion of Ge and Si atoms in Ge quantum dots (QDs) were estimated from the analysis of frequency positions of longitudinal and transversal optical phonons observed in the Raman spectra. Raman scattering by folded longitudinal acoustic phonons in the Ge dot superlattices was observed and explained using elastic continuum theory. An average size of Ge QDs was obtained from transmission electron microscopy measurements.