Third Alternatives
I have to disagree with Sean K. Reynolds (and everyone here, apparently). I think his arguement sets up straw men, and knocks them down...
In the FIRST place, the options he lists are NOT the only ones.
In the SECOND place, D&D has had called shots since 1e! (Characters sans helmets were hit in the AC 10 head 1 on D6; Bulettes shot under the raised fin had a lower AC at that point, unarmored heads were AC 10, Beholder's eyes could be cut off/shot out, etc.)
When I want to make a called shot, it isn't to do extra damage, it is to achieve some other SPECIAL EFFECT! For example, in one game, after being transported, the entire party was stunned. Mine recovered before anyone else, and found the defenseless party being charged by some orcs and a cyclops creature... Since no one else was even aware of the danger (let alone able to react to it), I asked the GM his rules for called shots, and tried to shoot out the giant cyclopskin's single eye... I figured a blind one might be easier to handle.
Now suppose that the critter's eye was no easier to hit (blowing away one of Sean's arguements), and the hit did no extra damage (blowing away the other). Suppose that all it did was normal damage, gave a -2 Circumstance Modifier to the To-Hit roll, and (if it hit the eye) also invoked the blindness penalty (or, in the case of a Beholder, caused that eye to cease functioning).
If True Strike bothers you, then make it unusable for this purpose. Seems simple enough.
1e only had a few called strikes; the head, bulette's under-fin, and beholders' eyes are all I can remember. Personally, I LIKE the idea of being able to wait until a heavily-armored creature opens its gullet, and firing an arrow down its throat, ignoring its Natural Armor and any Armmor/Barding being worn... Seems to me that the AC line on the stat block allows for this, and it makes a better game!
Are you a Fighter without magic, up against a Beholder? Take cover, and shoot out its eyes!
Are you a Halfling, hunting a Bulette? Better climb a tree! Otherwise, you won't be high enough to shoot it under the fin!
Are you a Dwarven Giant-Killer, trying to take on a giant at low levels? Blind him, then take out his limbs.
What needs to be done? Two things:
1) Determine the general To-Hit penalty for Called Shots. -2 Circumstance Penalty seems good, but maybe too low. -4 seems alright (as someone suggested, above). Another option might be to make it the only attack in a round, as you take time to line up the shot.
2) Determine the effects of each called shot. What can be affected, and what results are achieved with a hit.
Mongoose has already done this (although I don't like it, as you have to be level X to perform such feats). The 3e Rogue also has a 10th-level-plus ability that does STR damage to limbs.
There is certainly room for this, even in the abstract 3.x combat system. I was very miffed to find that I could not blind the one-eyed cyclopskin!