I didn't read all of the other replies, simply because the 9mm vs .45 debate is so common.
Here's my thoughts:
CARRY WHAT MAKES YOU COMFORTABLE! YOU WILL BE FINE WITH EITHER CHOICE!
Personally, I've been carrying a .45 caliber service pistol for my entire career as a police officer, but I wouldn't hesitate to carry a 9mm if the opportunity presented itself. With modern bullets both calibers perform very well, with a slight edge in expanded bullet diameter going to the .45, and a slight edge in overall penetration going to the 9mm.
My duty weapon holds 10 rounds per magazine, versus 17 in the 9mm. Honestly, I have every confidence in my ability to handle a situation with the first 10 rounds (at least if it is any kind of fight that I'm going to live through). Similarly, I have every confidence that a single modern 9mm bullet would be able to disable a bad guy as effectively as a single modern .45caliber bullet.
But, your question comes at an interesting time, as I was just pouring over some data from a recent wound ballistics workshop at my department. Here are a couple of interesting figures for you:
In 10% ballistic gelatin (calibrated to the FBI standard) we shot our 9mm and .45ACP ammo into bare gelatin at 10ft:
9mm +P 124grain Gold dot: 14.75" of penetration with an average expansion of .605" inches, and 100% weight retention.
45 Auto 230grain Gold dot: 12.75" of penetration with an average expansion of .704", and 100% weight retention.
So, in bare ballistic gelatin you lose 2" of penetration with the .45, and gain 0.099" of bullet diameter.
Through "heavy clothing" (FBI standard) the same bullets produced:
9mm: 16" penetration / 0.521" expanded size / 100% retention
.45ACP: 15.25" penetration / 0.687" expanded size / 100% retention
Through auto glass the same bullets produced:
9mm: 14.25" / .595" expanded size / 89.19% retained weight
.45ACP: 14" penetration / 0.629" expanded size / 97.83% retained weight
Based on the results that I witnessed firsthand, I'd carry either caliber with confidence! By the way, this workshop was the first time I had seen the Federal HST ammo, and it was VERY impressive as well.