My opinion is that the .40 is better than the .45 and 9 because it's newer and as Evan Marshall says (paraphrasing) "there are no bad loads". It runs at higher velocities than the .45, so expansion will be less problematic from compact pistols and the .40 can work in smaller frames and yield more capacity.

The 9mm needs the best modern ammo to hang with it's .40-something big brothers. It is however, the king of round count.

Really the 9, .40 and .45 are all great calibers and one should work as well as the next with the best modern loads.