Well, each have their merits and shortcomings in my opinion.
These views are from a FMJ only stand point not from a expandible bullet one:
7.62x39:
Good:
common cheap, plentiful.
Decent stopping power, especially with proper bullets.
Reasonably accurate to 400m.
Bad:
Not as good as fragmenting bullets (when and if they fragment).
Arcing trajectory.
Heaviest ammo and magazines of the 3
5.45:
Good:
Low recoil and muzzle flash.
I would guess better stopping power than a round fired from an M4, when the M4 bullet does not fragment due to early yaw cycle.
More accurate than the 7.62x39.
lighter than the 7.62x39
Bad:
Bullet does not fragment.
Not as easy to find as 5.56mm of 7.62x39
Reasonable accuracy to 400-500M
5.56:
Good:
Very available.
Less recoil than the 7.62x39
Best in the terminal ballistics dept. if bullet does fragment.
Accurate to 500M, more accurate than either Russian round.
lightest of the 3 for magazines and ammo
Bad:
Worst in terminal ballistics dept. if bullet does not fragment.
More expensive than the 7.62x39 but just as available in U.S.A.
In my experience I choose the 7.62x39 over all others. I talked to a few Afgans while I was there and most of them agreed that the 5.45x39 was not really that effective. One of them also laughed at the 5.56mm and derogatorilly said "Stinging bullet" an unflattering comaparison to the 5.45mm. I was offered on many occaisons a 5.56mm M4A1 and it carried one a few times (I also was able to get some 77gn rounds for it, that made it a litte easier for me to carry)-But I preferred to carry an AK-47S, AKMS, AKSU, or an AMD-65 in 7.62x39mm. The 5.45mm never entered my thought processes for carrying. But it is personal opinion for the most part. I also learned that carrying the steel AK mags in a chest rig got heavy quick-I found the Russian Bakelites much nicer to carry all day.