Upsides, down sides-

9mm uses a smaller, higher velecity bullet than the .40, but in terms of kientic energy applied to the target, the differences are small BUT statistically detectable. With expanding bullets of modern design, the playing field is leveled somewhat, but the .40 is still a better "stopper".

On the other hand, .40 is more expensive, harder to find, and more boisterous. You can buy more training ammo for 9mm. Which means you are going to be more confident to hit your target every time. Accessories that are picky about caliber, like magazines, are also more readily available, but there are few that are bore-specific between the two.

Personally, I think "stopping power" is about the most over blown thing in the world. In a defensive situation, I'm more concerned with putting the bullet where it needs to be to turn them off, RIGHT NOW!! I'd pick the 9mm just becuase I can get more bang for my training dollar.

But that is also from someone who used to break 13 necco wafers per magazine with his Hi-Power at the distance of the bedroom. On the range of course. :P