I think I'll post some houserules on the subject that I had put together last year, but haven't had the chance to use in-game yet (I was already running a campaign at the time, and haven't been able to start up a new campaign yet).
It puts a modest or high limit on the number of times a character can return to life, while providing a way to slowly stretch that limit over the course of several years in-game. Adventurers who run headlong into peril every week won't likely be able to keep up with the decline of their soul's resilience if they don't take pains to avoid dying most of the time. These rules also penalize characters for dying without kicking them in the nuts to do so, gaining negative levels and ability score penalties instead of losing levels or Constitution or whatnot.
Potential Changes To Death And Returning To Life
Each time a character dies and successfully returns to life in some way, even if only partially so, such as becoming undead, they suffer 1 point of Souldrain, plus an additional point of Souldrain for each level they would have otherwise lost from the process. Souldrain cannot be acquired any other way, and it can only be removed in a few ways. A wish or miracle spell will remove 1 point of Souldrain with each casting. A lesser deity can remove 1 point of Souldrain as a full-round action, an intermediate deity can remove 2 points, a greater deity can remove 3 points, and an overdeity can remove 4 points. A character's Souldrain total cannot be reduced more than once per year. Once a character's Souldrain total equals their Charisma score, they die immediately and their soul is utterly, completely, permanently destroyed, torn into its constituent energies and scattered across the cosmos, with absolutely no way to return.
Whenever a character might return to life in some way, they are forced to roll a Will saving throw against a DC of 5 + their Souldrain total, even if their current Souldrain is zero (DC of 5), and a failed save means they are not returned to any semblence of life, as their soul slips from the grasp of the magic. Whatever attempted to bring them to life or unlife still finishes and works normally in every way, except that the character who failed the save does not return to life or unlife. Whatever initiated the life-returning or unlife-animating effect will know that the character's soul slipped from the magic's grasp, and will know generally how much the character failed the save by. Another attempt may be made as normal, and these failures do not count towards any limit of the effect that would have returned them to life or unlife.
Any character with a Souldrain total higher than 5 will suffer a penalty on most Charisma checks and Charisma-based skill checks for social interaction with anyone up to 20 feet away. The penalty is equal to half their Souldrain total beyond 5, rounded up. For instance, a character with Souldrain of 6 suffers a -1 penalty, while someone with Souldrain of 14 suffers a -5 penalty. This is due to emanations from the character's battered and torn soul, which discomforts others around the character and gives them a slight negative feeling about the character. Additionally, this penalty applies on any saving throws the character attempts against energy drain of any sort, due to their weakened, vulnerable, tattered soul.
Potential Changes To Level Loss And Negative Levels
Characters no longer lose levels when returning to life, as noted above, but they do still suffer some penalties beyond Souldrain. Likewise, characters no longer lose levels from negative levels or level drain. Instead, when a character returns to life, they acquire a number of negative levels equal to the number of levels they would have normally lost from the return. Characters no longer lose actual levels from lingering negative levels, but instead all negative levels are semi-permanent, such that a character makes a single Fortitude save once per day when sleeping (or taking an equivalent rest period, if belonging to a race that does not sleep). The save DC is 15, and each time they succeed at the save, they recover from 1 negative level. Any time spent dead does not count towards this recovery time (but time spent as undead does count). Similarly, any level drain a character would normally suffer instead becomes an equivalent number of negative levels. Characters no longer die when their negative levels equal or exceed their actual level, but instead they fall into a coma until their negative levels are less than their actual level. They can still recover from negative levels in the same way noted above, but are helpless, unaware, and unable to act in any way, while nothing can remove the coma except for losing negative levels. However, they will still perish if their current negative levels exceed their combined character level and Charisma score.
Whenever a character returns to life by any means, including partial life such as undeath, they suffer a -2 penalty to all ability scores, and another -2 penalty to all ability scores for each negative level they acquire from returning to life (if any). These penalties stack with themselves and each other, and cannot be removed by any means except for the Newlife Recovery divine spell. Instead, the character's total penalty on ability scores from this effect is reduced by 1 point each week until it has completely faded. Any time spent dead does not count towards this recovery time (but time spent as undead does count). Death and returning to life are traumatizing experiences, and it takes time for the soul to adjust to its new body or newly-restored body.
Newlife Recovery
Conjuration (Healing)
Level: Cleric 6
Components: V, S, XP
Casting Time: 1 minute
Range: Touch
Target: One creature touched
Duration: 1 week
Saving Throw: Will negates (harmless)
Spell Resistance: Yes (harmless)
This divine spell hastens a character's recovery from returning to life or a semblence of life. For the duration of this spell, the touched subject (who must be either alive, undead, or in a similar state, other than dead) gains a +5 enhancement bonus on Fortitude saves made to recover from negative levels. Likewise, for the duration, the character reduces their ability score penalty for returning to life, undeath, or a semblence of life by 1 point every 3 days instead of 1 point every week, starting on the day this spell is cast. Casting Newlife Recovery on a character multiple times during the duration of a previous Newlife Recovery has no extra effect, as the spell does not stack with itself.
Experience Point Cost: The experience point cost for casting this spell is 600 experience points.