An interesting idea. How about this idea:
You roll a critical hit on your attack. It is time to roll to confirm the critical. You now have the option of making a called shot. Some type of size modifier of the size of the target is added to the necessary AC for confirming the critical. If you succeed in this the target suffers the effects of the called shot. Else, they suffer normal damage. You can forgo making a called shot, which will leave the target number for confirming the critical unchanged.
Example:
Arm, Leg, Trunk (lung, etc): +4 to confirm critical roll
Hand, Foot, Neck, Head: +8 to confirm critical roll
Eye, Ear, Finger, coup d'gras: +12 to confirm critical roll
So you roll a 19 while using a longsword, for a total of 27 against your foe (whom you needed 24 to hit). You now may roll to confirm your critical. You only need to make 24 (a roll of 16+) to do this. As an option, you can increase the difficulty of this attempt for different (additional?) effect. Due to only being able to roll as high as 20, in this example the best you could hope for is to make a called shot to an arm, leg, or the trunk (lung or other internal organs). If you succeed you handicap the foe and perhaps also deal normal critical damage.
Another example:
You roll a natural 20 (for a total of 36) against a foe you only needed to roll 10 to hit. Now, to confirm your critical, you need to make at least a 26 (a roll of 10). You could choose to aim for 30 (a roll of 14) if you wish to make the critical a called shot to the arm, leg, trunk, etc, or you could make it harder yet by aiming for a 34 (a roll of 18) to make a called shot to the hand, foot, neck, head, etc. If you fail you deal normal damage. If you succeed you deal additional (different?) damage.
A final example:
Against an overwhelmingly easy foe you only need to roll a 2 to succeed in the strike. You roll an 18 with a longsword and due to Improved Critical you have make a critical hit. Now it is time to roll a confirmation. You could go for something almost certain - such as a wound to the arm, leg, trunk (internal organs), but you want to make an example, so you you choose an hit to the eye - almost certainly lethal, or at least permanently blinding (in that eye). However, that requires adding +12 to the target number (of 2, for a required roll of 14 to confirm). This is almost ridiculously easy, but note that it would not have been available for either of the former examples, as a natural 20 on the confirmation would not have been able to reach the target number had +12 been added to it.
I'm not too sure about +4, +8, and +12. Perhaps +5, +10, and +15 would be a better option? Or maybe the +4, +8, +12 option will work?
As for the additional / different damage, it depends on how potent the called shot results would be. If a +4 type called shot merely hampers movement (ie: shot to the leg), then doing normal critical damage in addition to the movement hampering is not too much. If it causes dex damage then it should replace the normal critical damage (so that only normal damage and the called shot damage occurs), rather than stack with critical damage.
I see a +4 called shot as being inconvenient: hampering movement, giving a penalty to attacks or skill uses, and so forth. This is the one most likely to be most often used, so it shouldn't be too powerful. Reducing movement to half speed, say, or perhaps inflicting a -2 to attacks and skill checks using that limb, or maybe a -1 dodge penalty to AC - these are what I expect of a +4 called shot modifier. Maybe the penalty only lasts 24 hours, maybe it lasts 1d4 days, but it does not last over long.
A +8 called shot I can see actually removing the hand or foot - or damaging them so severely as to result in a severe penalty modifier for attacks, skill checks, etc using that limb. Unlike a +4 called shot modifier, I see the damage from this as potentially permanent rather than temporary / inconvenient. Magic might be required to heal the injury / remove the penalty. Or perhaps the penalty can be reduced to no worse than a permanent version of a +4 called shot modifier by using an attachment (peg leg, hook hand, etc). Significant ability damage (2d3) or minor ability drain (1d3) to a physical ability score sounds like a good measure of how debilitating these injuries are. If it is only ability damage, the hand is so bruised it takes days to fully heal. Or perhaps it is so broken that it cannot heal - or has been completely lopped off (thus drain instead to reflect this).
A +12 called shot modifier will rarely be used, as it means that the confirmation is normally a roll of 8 or less. Most foes the PCs go against will require more than an 8 to hit, so foes this can be used against are minor at best, inconsequential at worse. Thus, its affect should be equivalent to a coup d'gras - a permanent , debilitating penalty that requires magic for healing and restoration. Blindness, deafness, muteness (a hit to the throat), lameness (a hit to a tendon or knee joint, perhaps), inability to use an arm henceforth, ability drain of any type (including mental - reflecting a hit to the head), is the hallmark of this type of shot - presuming the PC doesn't use it for an immediate coup d'gras, slaying the foe outright.
Note that these modifiers might be used for other purposes as well: +12 to a shot to hit a rope at a distance, perhaps.
The system above was just now made on the spur of the moment, so it likely needs a bit of refinement. There are likely several issues I have not considered. I am presuming, for instance, that a typical CR encounter for a group of PCs will require the PCs rolling - at the minimum - at least a 10 or 11 to make a hit, with 14-15 probably being the more commonly needed roll against a CR appropriate encounter. Thus even if a critical hit is made, adding +4 to it will be potentially risky, and adding +8 will make it unlikely to succeed. Adding +12 should put it beyond the reach of a natural 20 for CR appropriate encounters. Only when the encounter is sub-appropriate CR should adding +12 the the roll to confirm be possible - and even then it should be several levels below the typical CR before it becomes practical to add +12 with any high hope of actual success.
If I am wrong on this then the roll to confirm modifiers need to be raised as necessary (perhaps to the priorly suggested +5, +10, +15?).