This has always been a sticking point for me especially in modern games. I like to call this the Kevlar Helmet situation.
We were playing a game based on a very GI Joe type of setting using the Cyberpunk 2020 Interlock game system. For those of you not familiar with that system, it revolves around rolling a die for your skill and another for your linked attribute and adding the results to meet or exceed a target number. In combat you would roll to hit usually verses an opposed roll. If you hit, you would roll a number of dice to see what damage your attack did then subtracted any damage resistance the target had. The only factor that went into damage was the damage factor of the weapon in damage dice. This is what I call a Random Damage system. The base damage of the weapon being the lowest result of the dice and the maximum being... well... the maximum result of the dice.
Now, the reason I call it the Kevlar Helmet situation was that one of our player characters named ASP or "Advanced Sniper Project" shot an NPC with a Barrett Light 50 sniper rifle with a called shot to the head. (Now, as a side note, I was at a gun show a few weeks before this and saw a three inch block of steel one of these weapons SHOT THROUGH!.) This direct hit, with a considerable margin of success, but did near the minimum amount of damage it could do, which was still considerable due to the 6d6 points of damage the thing put out. Yet the NPC's, being part of a wealthy military unit wore a Kevlar Helmet with a damage reduction rating. Due to this damage reduction the direct hit on the mellon with a 50 cal failed to kill the incredibly lucky private first class.
This derailed the game for a good amount of time as ASP's player was understandably incensed by this situation. He hit solidly square in the middle of the poor soldiers head with a massive bullet moving just under the speed of sound and failed to make the kill. The fact that he had to shoot the poor unfortunate bastard twice to end his insignificant NPC life wasn't really the point. The real sticking point was that it was still possible to do crap damage on a direct hit with a called shot.
From then on I had a pretty real problem with systems that did not factor margin of success into damage. I guess I was just spoiled by games like Shadowrun or the White Wolf system that factored margin of success in attack damage. It is quite possible in this system to kill someone outright with a knife or at the very least incapacitate them. Which is very likely to happen if a person gets stabbed. As a matter of fact, my Street Sam walked into a restaurant with no weapons and killed someone with a steak knife. Now that is heroic and down right cool. No way that would be possible with a 1d4 damage weapon.
Our GM argued that the called shot did increase the base damage of the attack, thus overcoming the increased target number in order to enjoy that bonus was in essence a reward for a "finesse" shot. This sort of up front reward does not really sit well with me at all, but it seemed an acceptable enough explanation to keep the game rolling.
Things like called shots, critical successes and similar mechanics seem too arbitrary. The idea that your weapon will do an increased damage 5% of the time with no real element that rewards an increased level of skill is not really heroic. "Luck will save a man, if his courage holds." or so says Buliwyf, but relying on luck really reduces the badass factor and having to call shots makes for a bit more cumbersome a system than needed.
In the final analysis, its important to make the heroes of a story feel heroic. The characters abilities should be the key factor in resolving conflicts, combat or non-combat.