I don't think anyone will argue that shot vs. shot, 9mm is not as good as .45. I think the arguments come from 9mm having a lot of other advantages over .45 (capacity, recoil/controllability, pistol size for concealability, price of practice ammo) and people trying to weight the advantages vs. disadvantages of each round. I don't think the bullet diameter difference is very significant and I think it's focused on way too much (.07", and with higher velocity 9mm will probably expand more reliably). I think the primary advantage of .45 is the bullet weight for higher momentum for penetrating bone, muscle, and fat and remaining on course. If you only ever hit soft tissue, I think the 9mm is better than the .45 because it will penetrate just as far and do just as much damage, only you have all the other advantages as well. I think people question whether or not the 9mm will be deflected off course by bone though because of the ligher weight bullets. The .40 is kind of middle of the road because it's velocity, weight, capacity, and recoil are somewhere between the 9mm and .45.
As far as "knockdown" power, there really isn't such a thing. A bullet will exert the same force on your target as it exerts on your hands in recoil "IF" it's stopped in the target. That in itself is not enough to knock anyone down (i certainly don't know anyone that falls down from the recoil of shooting a gun), and if a bullet passes through someone it won't even dump all that energy in them.