I carried both the .45 and .40 cal glocks at various times as duty weapons...
The .40 cal has basically the same ballistics as a .357 magnum and is a great round. The .45 is a great round also but lacks the penetrating power of the .40 or .357
Cor-Bon makes a nice hopped up round for the .40 cal also which travels at about 1350 fps.
Not to be gory here, but I've witnessed a few shootings where the .45 failed to stop the suspect immediately, and the .40 was pretty much a one shot drop.
Of course a well placed shot from just about any weapon will stop someone in their tracks, you don't always have the time to take careful aim, and rely on the stopping power of the round.
My vote is for the .40 cal