D&D and other d20 systems apply no penalty to characters who are mortally wounded and then tended back to health. There are in fact no mechanics in the system for injuries that maim and hamper a person after they have otherwise healed.
Similarly, the D&D rules don't have any room for most characters to be laid low from wounds after the battle, perhaps as they crawl into a fort and collapse with a message clutched in their dying hand.
The following is an attempt to introduce rules that allow for more dramatic injuries, without upsetting the game balance too much.

Please let me know what you think of the rules in general, the DCs in particular and all that stuff.

Ta!

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Maiming
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Whenever you take direct damage that reduces your hit points from a positive amount to a negative amount, you run the risk of being maimed in some way by the injury. (Area effect damage does not maim.)

Roll a FORTITUDE save DC 15 + amount of -ve HP. Success means you are merely hurt and probably unconscious and dying. Failure indicates that you have been maimed.
Maiming never reduces HP, but usually incurs an ability penalty.

Roll 1d6 and consult the table below:
1: head: 1d4 INT damage
2: left arm: 1d4 STR damage, cannot use arm to wield weapons
3: torso: 1d4 CON damage
4: right arm: 1d4 STR damage, cannot use arm to wield weapons
5: left leg: 1d4 DEX damage, 1/2 movement rate
6: right leg: 1d4 DEX damage, 1/2 movement rate

Maimed characters can be restored to health by magically curing the ability damage incurred in the maiming, usually with Lesser Restoration or a similar spell, or with the Surgery application of the Treat Injury skill (DC20).
Natural rest and healing will not restore the maimed character to full health.



Imperfect healing
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When a character uses the Treat Injury or Heal skill (depending on game system) to stabilise a patient (or restore lost HP, in d20 modern), the GM rolls the check in secret.

Stabilising:
9 or below, the patient is not stabilised and you know you have failed.
On a 10 to 14, the patient is stabilised, but imperfectly. You can only see that you have stopped the bleeding. If he takes any strenuous action, such as running, fighting, climbing, lifting more than a heavy load, he loses 1 HP per minute until treated again. The patient and any other observers can attempt a Spot check (DC10) each time a HP is lost to detect her worsening condition.
On a 15 or higher, the stabilisation is fully successful. You can only see that you have stopped the bleeding.

Restoring HP:
9 or below, the patient is not healed and you know you have failed.
On a 10 to 14, the patient 1d4 gains temporary HP, but imperfectly. You can only see that you have stopped the bleeding. If she takes any strenuous action, such as running, fighting, climbing, lifting more than a heavy load, she loses the temporary HP at a rate of 1 per round. The patient and any other observers can attempt a Spot check (DC10) each time a HP is lost to detect her worsening condition. If the patient is allowed to rest, the temporary HP are lost at the same rate that the permanent HP are gained.
On a 15 or higher, the restoration of HP is fully successful. You can only see that you have stopped the bleeding.

Imperfect healing can be rectified with a second, more successful skill check.



Worsening wounds
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Some wounds can bleed long after they are inflicted, putting a character at risk if not treated.

If you take more damage than your CON ability score + character level in a single physical attack (that is, not energy damage), then you must make a FORTITUDE save DC 10 + number of dice used to inflict the damage (if the damage is a fixed amount, divide it by 4 to find the save DC modifier).
A successful save means you just take the damage. A failed save indicates that you have taken a worsening wound, and will bleed 1 HP per minute until healed. You (or any other observers) can attempt a Spot check (DC10) each time a HP is lost to detect your worsening condition.
Worsening wounds must be treated as if stabilising the patient.
Magical healing removes a worsening wound if the caster also succeeds in a Treat Injury of Heal check, DC15 - level of the healing spell.