I wanted to share a ton of alternate options and suggestions created by reddit user LokiOathBreaker (shared with permission, of course). These are all created with the Pathfinder Role Playing game in mind, but can pretty easily be adapted to a bunch of alternate systems.
This system assumes that all residents of Salt in Wounds live under the threat of potential mutation, though the rift between rich and poor is quite evident. The threat of mutation is tracked by how much 'Tarrasque taint' or simply 'taint' people carry within them.
Simply being within Salt in Wounds long enough exposes a character to the Tarrasque's essence. The water, meat, even the very air they breathe is tainted to varying degrees and as such Taint automatically increases by 1 point per week of living in Salt in Wounds. It must be mitigated or reduced if one is to avoid mutation
Worse, those who work closely with unprocessed Tarrasque material, such as harvesting and processing laborers, alchemists and individuals of similar occupations gain 1 additional point per week even if no other incidents occur.
Active Taint gain comes from more immediate exposure, which can come in many forms. When it occurs, roll 1d6 to determine the potential Taint gain. A character resists said gain with a Fortitude Saving Throw (with a DC appropriate to the intensity of the exposure) and, if successful, the gain is reduced by half to a minimum of 1.
How does one get rid of Taint, however? The Taint score may be reduced in a variety of ways:
The safest and most secure method is available to characters who are below their Mutation Threshold and have not been afflicted by any mutations. They may reduce their score by one point for each week spent away from Salt in Wounds. Consequently, members of high society often take long holidays, whether they are still pure or merely going through the motions to better hide a minor mutation.
A variety of 'cures' exist. Alchemical concoctions, special dieting regimens, even dubious purifying rituals. While many 'miracle cure' fakes are sold, some are known to be effective.
The more readily available variants involve a saving throw (fortitude or will, depending on the nature of said cure) with a difficulty equal to the current Taint score. If successful, they reduce taint by 1d3 and are Fatigued for the rest of the day.
More expensive and potent cures exist. They may remove more taint, lower the saving throw DC, or both.
So far, no feasible means to reliably remove or cure taint through magic have been found, though 'Purify food and drink' spells are an integral part of meat processing in Salt in Wounds.
(Side Note: Magic can of course help with Taint, but requires spells that are out of reach to most. Very high level magics such as Wish/Miracle would be effective, as would becoming an intelligent undead -- becoming a ghoul is readily offered in Salt in Wounds, but not exactly desirable -- or keeping an untainted clone on backup to transfer your mind to.)
A way to resist taint gain in the first place, rather than lower it afterwards, is Inoculation. Taint Inoculation is generally only used by those most at risk, offering tangible benefits in exchange for accepting taint into your body: one shot immediately causes 1d6 taint (which may be halved with a Fortitude Saving Throw vs. DC 15), but protects against the weekly gain for one whole month and reduces any other taint gain during that time by 1 to a minimum of0.
Taint and Races
Some races are less susceptible to taint, others more. Particularly long-lived/unaging races or those that could already be considered 'tainted' in some way such as the plane-touched races, dhampirs, changelings, etc. may add +4 to their mutation threshold. Particularly short-lived or mutable races such as most goblinoids take a -2 penalty to their mutation threshold.
Undead are unaffected by taint. If their bodies remain as they were, they retain any physical mutations they already have, but their taint score is effectively frozen the moment they undergo the transition. If they are later revived, their taint score unfreezes.
(Side Note: Some crafty wizards have made good use of the Undead Anatomy spell thanks the local ghoul population. While generally known to those educated in the arcane arts, those who employ the spell generally do not share it. It's considered too costly and short-lived a solution to waste on the workforce and most nobles generally do not desire to be turned undead, even temporarily.)
Starting Taint & Taint Traits
To incorporate taint in character creation, players roll 2d6 to determine their starting taint, unless otherwise specified by a chosen taint trait.
Frequently Exposed: The character has been exposed to Tarrasque taint more frequently than others -- whether by working in with the Marrow Miners, living in the slums and drinking the tainted water there, eating improperly processed meat or gorging on the regular kind for years. They add 5 points to their taint score, may choose one superficial change (minor) and gain a minor advantage*.
Taint Infusion: Your character has been exposed to a life-threatening amount of taint, whether through experimentation, accident or even an attempt on their life. They are now thoroughly tainted and mutated, but have also developed a resistance against further mutation. They add 10 points to their taint score, may choose two superficial changes (minor) and roll once on the Major Mutation chart. They gain +1 bonus to saving throws against further mutations.
Mutation Maniac: Your character is particularly mutable. They gain 5 points to their starting taint and receive a -2 penalty against mutation saves, but in exchange add +2 to any rolls on the mutation chart, increasing the likelihood of a benevolent mutation.
Pure This trait must be decided on before rolling for initial taint score. The character has not been exposed to as much taint as others and begins with a low taint score of 2. They also reduce all taint gains, except the weekly, by 1. As they do not have the built-up tolerance to taint that others possess, they suffer from a -1 penalty to saving throws against mutation.
Taint Tolerance This trait must be decided on before rolling for initial taint score. The character begins with a taint of 10, but increases their Mutation Threshold by 2.
Aberrant Beauty While your character is not immune or resistant to mutations, they tend to manifest in a manner that, while still alien and potentially monstrous, is strangely attractive. They gain a +1 taint bonus to Bluff and Diplomacy rolls against those attracted to their gender, but only after they gained their first non-flaw* mutation. This trait does not override mutation flaws* with social impact and otherwise only works for minor and major changes.
Mutant Brute While some mutants look positively wretched, your mutations only serve to make you scarier. You gain a +2 taint bonus to Intimidate rolls, but only after gaining the first mutation.
A character has a Mutation Threshold of 10+Character Level. If their Taint increases beyond that, they are at risk of Mutation and must roll a Fortitude Saving Throw vs. Mutation each time they gain taint, including the initial gain that put them there.
If they fail their save, they must roll for a minor mutation.
If a character is in excess of their Mutation Threshold by 5 points, they roll for major mutation instead. If they are so by 10 points, they roll for an extreme mutation.
If a player rolls a mutation that their character already has, they may either reroll or accept exacerbating changes to that feature that make it more obvious, alien and hideous. In the same vein, if they already possess a feature the mutation would have granted them (such as claws), they may do so as well. A functional version of a nonfunctional mutation overrides it.
All Mutation-related bonuses or penalties are of the 'taint' category and do not stack with each other.
Natural 1 Reroll for a Major Mutation with -3 modifier
1-5 Gain Minor Flaw*
-6-16 Superficial Changes (minor)-
17-20 Gain Minor Advantage*
Natural 20 Reroll for a Major Mutation with +4 Modifier
Natural 1 Reroll for an Extreme Mutation with -3 modifier
1-5 Gain Major Flaw*
-6-16 Superficial Changes (major)-
6-9: Body 10-13: Limb(s)
17-20 Gain Major Advantage Natural*
20 Reroll for an Extreme Mutation with +4 Modifier
1-5 Gain Extreme Flaw*
-6-16 Superficial Changes (extreme)-
6-9: Body 10-13: Limb(s)
17-20 Gain Extreme Advantage*
Superficial Changes Defined
These mutations are usually alien and monstrous to varying degrees. It's not uncommon for low-class citizens to show a small number of minor changes, but those who are disfigured by a multitude of minor changes or worse, demonstrate major or extreme changes, are generally shunned by high society (unless they also possess the Aberrant Beauty trait, see further below).
Since these changes are only superficial, this does not reflect upon their actual statistics. However, NPC starting attitudes may be affected when appropriate.
Body Changes are primarily changes to the full skin area or mutations of the torso. They cannot include changes to areas that are covered by the other two categories.
Limb Changes affect the arms, hands, legs, feet and other extremities such as tails or tentacles.
Head Changes are all changes centering on the head, primarily the eyes, nose, hair, lips and tongue.
The exact decision on how a superficial change manifests can be reached in multiple ways, whether through dice rolls or discussion between player and GM (or combinations thereof), depending on sensibilities and willingness of the players to accept the body horror of the setting inflicted on their own characters.
One such way that leaves both a random element and some design choice on the players' end is to create a chart of potential changes for each level of mutation in coordination with the players, then roll on those. Taking this a step further, for a particularly creative group, one could create a unique chart for each character.
Mutation and Taint Cures
There are ways to remove, revert or allay some physical mutations, though most are arduous, complex, criminally overpriced or plain dangerous. Psychological changes caused by mutation are much more difficult to cure, though their effects can sometimes be mitigated with alchemically created medicine and/or spells.
Very invasive and painful, but also very effective for mutations that are largely self-contained. An extraneous limb may be cut off, an undesirable growth removed and healed over, poison glands taken out and more. Once the mutation has been cut, magical or alchemical healing can take over, though in some rare instances may cause the unwanted mutation to return instead (roll a d20 upon surgery, a 1 means that future healing will restore the mutation until the surgery is redone, which allows a new roll). Surgery required a skilled surgeon and a Heal check of varying, though always high, difficulty.
Reliable, readily available magic to remove mutations does not exist, just as with taint removal. Again, wish spells can deal with mutation, as can a clone spell cast before mutation occurred. Any spell that permanently and fully transforms the body into a different one, such as Baleful Polymorph or Polymorph (Other) also removes physical mutations, though it does not affect the taint score and new mutations may occur. It's advised to keep note of the previous state of mutation when affected by such spells, as breaking the transformation will cause a reversal -- should the polymorphed state mutate more badly than the original, it may even be desirable to break the spell.
Alchemy can be used in the same way as spells above if suitable Extracts are available. Additionally, it can be attempted to revert mutations through extensive research of the subject and concocting a countermeasure specifically designed to do so. This should be done through multiple Craft Alchemy checks made in secret by the GM over the course of a week and require both alchemist and subject to invest one hour of their time each day exclusively to the task. The Craft DC should depend on severity of the mutation to be reversed. If all are successful, a reversal becomes possible, the exact means of which (an injection, or series thereof, a potion, a powder, surgery combined with any of these, ...) are left up to the alchemist. Just as with surgery, roll 1d20 upon taking the cure, a 1 means that healing will restore the mutation. If not all checks are successful, the cure fails. If more than half of the rolls are unsuccessful, a blunder occurred and the subject must immediately roll a saving throw vs. Mutation or gain a new mutation of the same level.
The poor man's fix. Sharp teeth and claws can be filed to look more normal at a casual glance, hair-spines cut away with a sharp razor and scales rubbed off. These are always unpleasant and usually either temporary or noticeable on anything but a very cursory examination. They are, however, cheap and readily employed.
(Side Note: Mutations that grant regenerative properties always quickly restore the mutant to his fully mutated state. Only permanent polymorph effects, Wish/Miracle or Reincarnation can help them return to a semblance of normalcy.)
*Note: LokiOathBreaker has not compiled a list of flaws and advantages. I'll post it when he does. In the meantime, look to the list of weal (for advantage) and woe (for flaw) mutations as inspiration.