A hartree is a unit of energy used in molecular orbital calculations. A hartree is equal to 2625.5 kJ/mol, 627.5 kcal/mol, 27.211 eV, and 219474.6 cm-1.
The energy reported from a calculation is the energy for the separation of the molecule to nuclei and electrons. For example the HF/6-31G* energy for CH4 is -40.195172 hartrees, which refers to the energy for the reaction CH4 => C6+ + 4 H+ + 10 e-
For semiempirical calculations (AM1, PM3) the energy is reported in hatrees, but the energy refers to the heat of formation for that species at 298 K. For example the PM3 energy for CH4 is -0.020766 hartrees which can be converted directly to a heat of formation of (-0.020766 hartrees)(2625.5 kJ/mol/hartree) = -54.5 kJ/mol.
More on units and conversions can be found near the end of the page discussing thermochemistry (Section I.D.2)