9 and 45. All three calibers are effective, so it comes down to choice in firearm. I buy guns I'd like to have in my casual collection, not as part of an arsenal, but for the unique features of the gun.
The .45 is for the 1911. I have one, and in my opinion, if you are going to have any 1911s, you need 1 in 45.
9mm for the rest. I have an interest in both function and historical significance, and there is much more overlap in 9 than 40. I could have a Sig, Beretta, CZ, S&W 3rd gen, Browning Hi Power design in either caliber, but they were all designed around the 9; so mine are in 9mm. I like the older designs too, so ammo will interchange with my S&W 39 and Star B Super, and if/when I can come across a Luger, Mauser, Radom Vis, etc, they can also use the same ammo.