Back on my soap box...
I actually think that this question has a quantifiable answer (and I am actually quite interested in the counter-arguments that may get posted in return). That is, the proper choice is the one that allow you to carry more rounds in a given configuration. And that answer is generally 9mm.
Why? Assuming that all three cartridges (9,40,45) evolve equivalently regarding expansion, speed, bullet design, etc., most on this forum, and others, cite that shot placement is the most important parameter in the effectiveness metric.
But most shooters (LEO's, concealed carriers, military, me I expect) are terribly inaccurate with their handgun when the adrenalin is flowing. Numbers of far less than 50% on target are quite common in a shootout.
So, versus a bit more mass, or somewhat more expansion of a 40 or .45 versus a 9, I'd just like to make sure I have more shots so that I might actually hit the target. And I suspect that is a good general rule.
By the way, this rule applies to LEO's, mils, and citizens who are not living in areas or under guidelines that restrict their magazine capacity. In those cases (e.g. CA where the capacity is 10), the rule flips and instead biases to the largest round you can carry, as long as you can carry the maximum allowed. So, it would be .45 in those cases.
B