I'd say the .45
Neither one can pierce body armor, but the Parabellum rounds can overpenetrate unarmored personnel. This means that they go through a person without imparting all of their energy=less stopping power. The big ol' .45 hits ya, and knocks you down. Furthermore, the subsonic .45 rounds are more silencer friendly.
I also think I read that Special Forces troops were given the chance to keep their 1911's instead of getting new Beretta's, and they opted for the .45
For home defense, though, it is a hard call. The .45 pistols out their have a lower ammunition capacity than do the 9mm pistols, so with a .45 you need to make your shots count--though, when they do, they count BIG TIME.