As far as pistol caliber, I like the .45 better because I can hit a target better with it than a 9mm. That is because for several years, the only gun I ever shot with was a 1911. The only 9mm i've ever owned or shot was a Sig226 and 228, and I don't like pivoting triggers as much as the straight pull trigger 1911 I think this aspect of the 1911 is very good, at least for me. The other 9mm was the HK P-7 and the area under the barrel heats up pretty fast with rapid firing and you couldn't hold onto it very long without letting it cool off. I owned a Glock but never shot it much.
I don't think one round is that much better than the other when it comes to "handgun battle" ranges, whatever they may be. If the 9mm penetrates so much, then why is issued? I've read that the .45 is "inherently accurate" over the 9mm, but I think that is mostly for the target/national match shooters and their reloads, not really that important an aspect for gun fights.
Yes, I prefer a 45 because it is what I like to shoot, but in a gun battle, I think hitting the guy in a vital area is more important than the caliber. Hit the brain at 20 feet with a 45 or 9mm, does it really matter that much if it is a 45 or 9mm hollowpoint?
As far as 5.56 and 7.62 for a CQB weapon, I'd probably choose a 5.56. Actually, I'd probably go with the 9mm. For a long range sniper weapon out to 6 to 700 yards, the 7.62. For urban (out to 300 yards), or shorter range sniper weapons, 5.56 or 7.62 would do. But I still think it is the shot placement that counts.
Harrydog pointed out that caliber choice sometimes depends on the type of gun abd I agree. Most 7.62 weapons are big and long (m-14, FNFal, HK91/PGS1/MSG90, bolt guns M40A1 or 3, etc...). Is the FNFal a good CQB weapon? You could use it, but it probably wouldn't be a first choice. 5.56 weapons are a little more compact (M-4).