If I could only have one gun it would be a .357 mag.
I really love the .45 ACP. It is usually more accurate than other calibers (don't know if its the cartridge or the guns). It has better stopping power (though it may be mainly theoretical, in real life situations both will stop a bad guy with proper shot placement and with poor shot placement the gad guy will still be standing after being hit with either).
However, if I could only have one auto I'd pick the 9mm (though right now I only have one and it's a 1911 in .45 ACP- go figure). I had a Ruger P89 in 9mm and really wanted the .45 so I traded (now I really wish I had both or, barring that, had just kept the Ruger for the reasons stated below).
With good quality defensive loads the 9mm can be nearly as effective as the .45 (and effective enough in most situations), and you'll certainly be fine with +P or +P+. With cheaper practice ammo you can pay almost half as much as the cheapest brands of .45 ammo. It seems to me that the only caliber with the same versatility (more versatility) is .38 spl. Also, 9mm guns seem to feed more reliably than .45s (just my observation, probably haven't shot enough of each to say for certain). For these reasons I've been advising my friends who are thinking of buying guns to go with the 9mm if they buy an auto (it will be the only one for a while and may be the only gun they ever own so versatility is good).
Oh yea, the .40 is good too.
Though it seems a compromise that takes some of the best features of both and throws them away. It isn't quite as powerful as the .45 (though it has very good stopping power). It isn't quite as versatile as the 9mm (somewhat more stopping power, though the better 9mm loads are close, and you don't have the cheap practice ammo with the .40 that the 9mm has- in fact ammo is in the .45 price range). If I could only have one auto I don't see that I would ever pick the .40, though as a second or third auto it may be nice. I can see picking it for some specialized concealment duties (it may be nice to have the extra power of the .40 in a small backup gun since they tend to have a small magazine capacity- I'm thinking the Kahr MK40 here) but a gun with such a specialized use would not be suitable as an only gun.
So I guess my vote is for both the 9mm and .45. If you must narrow me down, theoretically I vote for the 9mm but in real life I picked the .45. How's that for commiting myself.