We present a comprehensive spin-density functional modeling study of the structural and electronic properties of donor-vacancy complexes (PV, AsV, SbV, and BiV) in Ge crystals. Special attention is paid to spurious results which are related to the choice of the boundary conditions (supercell-cluster approach), the resulting band-gap width, and the choice of the points to sample the Brillouin zone. The underestimated energy gap, resulting from the periodic conditions together with the local-density approximation to the exchange-correlation energy, leads to defect-related gap states that are strongly coupled to crystalline states within the center of the zone. This is shown to produce a strong effect even on relative energies. Our results indicate that in all E centers the donor atom occupies a nearly substitutional site, as opposed to the split-vacancy form adopted by the SnV complex in Si. The E centers can occur in four charge states, from positive to double negative, and produce occupancy levels at E(0/+)=Ev+0.1 eV, E(-/0)=Ev+0.3 eV, and E(=/-)=Ec-0.3 eV.