Appearance energies of all parent ions and several fragment ions produced by electron impact ionization of the isotope systems H-2/D-2, H2O/D2O, and C6H6/C6D6 were determined with high precision using a dedicated high-resolution electron impact ionization mass spectrometer. The determination of the appearance energies from scans of the ion signal as a function of electron energy in the near-threshold region of each ion utilized a fitting and analysis procedure that has recently been successfully applied to the determination of appearance energies of singly and multiply charged rare-gas ions and several molecular ions and cluster ions. The experimentally determined appearance energies are in good agreement (i) with theoretical calculations that we carried out using standard quantum chemistry codes and (ii) with appearance energy values listed in standard reference data tables (to the extent that tabulated values are available). We find isotope shifts for all three systems ranging from a few meV for the parent ions to a few hundred meV for the fragment ions. The deuterated species always have the higher appearance energy. The present results for H2O/D2O and C6H6/C6D6 do not confirm the larger isotope effects that were reported earlier by Snegursky and Zavilopulo [Nucl. Instrum. Meth. Phys. Res. B 126, 301 (1997)].