9mm Luger (9x19mm Parabellum). Most times I have encountered a handgun, it is a 9mm pistol. This caliber is very popular among all the gun manufacturers. I can hear some of the gun aficionados saying that there are better calibers out there, but go to any gun range, most guns on the stations are 9mm pistols. I sometimes see .45 ACP on a 1911 style gun, some .40 SW, .380 ACP, 10mm, some magnums like .357 and .44, and the rare FN 5.7 (popularized by CoD MW3) but 9mm dominates.
I am not saying that 9mm is the best caliber. It is the most common. If I had to carry a handgun for survival, the calibers of choice would be 9mm and .45 ACP, though a .44 Magnum packs an insane punch and will kill with one shot placed appropriately. I am more than likely to find additional 9mm ammo more frequently than anything else in a survival situation.