Placement. Not a big difference between them truth be told. Some .45 guys hate this, since they're spending almost 2x the amount of money on ammo compared to the 9mm guys. (no, not counting reloading)
Fact of the matter is, and like others have mentioned, handgun is a mediocre stopper. It should be used as a last resort, and even then should be used to either
1.get yourself out of the situation
2. get yourself to a bigger gun IE shotgun or rifle.
But since you asked my opinion on caliber, and what's a good anti-personell round, I'd opt for 12 gauge 00 buckshot with 2 and 3 quarter inch shells. That's 9x 9mm balls traveling at 1325 fps.
My 2nd load of choice would be a 1 oz slug (.74ish) caliber in diameter, clocked in at 1600 fps, you know, if i really need penetration.