I think with the way things have been as of late you can kind of judge a calibers popularity by how many guns of that caliber are setting of the LGS shelves and if you can get ammo for it. This may be unscientific but, the 9mm is surely popular as it for the most part has always been. The .45 ACP has always been popular with police and those that could carry it. .40 S&W did have a surge of popularity but, better 9mm ammo slowed that surge IMO to a trickle.
Educated gun shoppers know that .40 S&W does not offer much over 9mm which is cheaper and has less recoil. So more and more are just buying either 9mm or .45 ACP.
I see much less selection of 45's and 9mm's at my LGS then I do 40's. The Cabelas had nothing but 40's for sale in the "Gun Library".
I own a 40 cal but it's a 10mm!