A systematic micro-Raman study of the atomic substitution effects has been carried out on single crystals of MgB2, including C-doping for B and Li- or Mn-doping for Mg. The spectra of C (electron)-doped compounds exhibit remarkable differentiations with respect to pure MgB2, and new bands of E2g and A1g/B1g symmetry play the dominant role in the substituted spectra. We have observed a two-mode behavior apparently driven by the electron–phonon coupling strength and associated with an electronic topological transition of the σ bands. On the other hand, Li (hole) and Mn (magnetic impurity) doping do not seem to affect the well-defined broad band at 600 cm−1. Combining Raman investigations and T c -interdependence shows that this band is not related with the transition temperature, questioning its relationship to superconductivity in diborides.