From what I can gather, you are going to make a special rule.
I suggest that it be recovery similar to non-lethal damage similar, but (taking a page from something I found from pathfinder) a condition that reduces constitution for awhile afterward.
(Edit 2: A thought on how it could be done
A character who falls unconscious (0hp) from suffocation or strangulation becomes fatigued.
A fatigued character can neither run nor charge and takes a –2 penalty to Strength and Dexterity. Doing anything that would normally cause fatigue causes the fatigued character to become exhausted. After 8 hours of complete rest, fatigued characters are no longer fatigued.
A character who is dying (-1 hp or more) from suffocation or strangulation becomes exausted.
An exhausted character moves at half speed and takes a –6 penalty to Strength and Dexterity. After 1 hour of complete rest, an exhausted character becomes fatigued. A fatigued character becomes exhausted by doing something else that would normally cause fatigue.
)
(Edit:
Homebrew spell that makes people who are defeated by it fatigued.
The pathfinder thing that mentions conditons Reproduced below:
Hit points represent your character's ability to avoid lethal damage. When you reach zero hit points or go negative, you gain a negative condition at the discretion of the GM.
For example:
Grignr the Barbarian faces off against Sargon the Sorcerer in the public arena, a dispute over the ownership of some gem. Grignr fells Sargon with one mighty blow of his axe, slamming him to the ground. Sargon's leg is broken, reducing his move rate and giving him -2 on all rolls, including his Concentration check to cast, due to the excruciating pain. Sargon musters his strength, makes his concentration check, and casts a maximized sound burst on the hapless Grignr, knocking him below zero. He makes his Fortitude save against the stun effect of the spell, but now has a concussion, lowering his rolls by 4, including his initiative while he desperately attempts to clear his head. Grignr aims another mighty blow at Sargon, critting again, and neatly splits him in half.
Healing
Hit points heal fast. With an hour's full rest, you'll get them all back. Conditions require more work. Simple conditions like a light fracture or a minor burn can be alleviated over time with an appropriate Heal check or immediately with a cure light wounds. More serious conditions require more time, better Heal checks, or stronger healing spells.
Healing spells still cure the same number of hit points.
For example...
The spell cure serious wounds has two effects. First, it can be used to cure a number of hp. Second, it can be used to remove certain negative conditions, such as a broken bone. If someone has no hp and has a broken bone, cure serious wounds will both heal the broken leg and heal hp. If a cure moderate wounds is used, it will only heal the hp damage, not the broken leg. Proper application of the Heal skill, together with rest, can downgrade negative conditions over time. So if you broke your leg a few days ago, had it set and splinted, and haven't been walking on it, it could be downgraded to a moderate wound.
Sample Conditions
* Black eye / swollen eye / blinded
* Ringing in your ears / deafened
* Stunned / Concussed / Unconscious
* Light fracture / Broken Bones / Compound fracture
* Minor blood loss / serious blood loss / critical blood loss
* Minor burn / serious burn / critical burn
* Wheezing / choking
* Exhausted / slowed / paralyzed
* Dead
So, to sum up...
1. There are no negative hit points.
2. Once you run out of hp (or an attack takes all of your hp, plus some), you gain a negative condition of the GM's choice.
3. Conditions are cumulative, and will lead to character death unless they are tended to.
4. There is no complete list of conditions, as characters have such unique methods of getting in trouble.
5. NPCs will most often receive the condition "dead".
6. The Heal skill treats conditions and helps you determine their severity, and therefore what spell is best suited to tend to it.
7. Hit points heal fast. Conditions take treatment and time, or the appropriate level spell.
Side note - feats and abilities that affect negative hit points will need adjustment. For example. Die Hard now allows you to ignore a single negative condition.
Strangulation rule made by some random guySRD. For the spoiler belowSuffocation
A character who has no air to breathe can hold her breath for 2 rounds per point of Constitution. After this period of time, the character must make a DC 10 Constitution check in order to continue holding her breath. The save must be repeated each round, with the DC increasing by +1 for each previous success.
When the character fails one of these Constitution checks, she begins to suffocate. In the first round, she falls unconscious (0 hit points). In the following round, she drops to -1 hit points and is dying. In the third round, she suffocates.
Slow Suffocation
A Medium character can breathe easily for 6 hours in a sealed chamber measuring 10 feet on a side. After that time, the character takes 1d6 points of nonlethal damage every 15 minutes. Each additional Medium character or significant fire source (a torch, for example) proportionally reduces the time the air will last. When a character falls unconscious from this nonlethal damage, she drops to –1 hit points and is dying. In the next round, she suffocates.
Small characters consume half as much air as Medium characters. A larger volume of air, of course, lasts for a longer time.