Let's start with three.
One is a point, two is a line, three is a shape. The Greeks were big on three and its multiples, at least partially for that reason, and this might be why we in Western civ have such a rough time not thinking in terms of threes. It certainly seems intuitive, from the perspective of the reality our language constructs: thesis, antithesis, synthesis. Once you have a thing, it's an intuitive leap to its opposite or absence, and an intuitive leap from there to the integration of the two. We see other arrangements as well: paper-rock-scissors is another one, appearing in Eternal Darkness as flesh-mind-spirit, the warrior, the alchemist and the wizard. Father, Son and Holy Spirit is the big one, of course, the one we can't unthink even if we want to. Metropolis refashions the trinity as head, hands and heart--suggesting a relationship between the three largely consistent with C.S. Lewis' description of the trinity itself. That which begets, that which is begotten, and the love between them, an animating force that is, itself, a person. The mind that conceives, the word that is spoken into being, and the breath that constitutes the connection between the two.
How does this relate to videogames? Mostly via a simple assertion: binaries are fucking boring. It's easier to make interesting relationships between three signs, characters, or factions than between two. And consequently, most modern RPGs and many adventure games are based around three primary stats or paths. Generally, it breaks down in terms of physical, mental/magical, and...other. Often it's agility, which is associated with stealth and thievery; agility essentially being an intuitive connection between mind and body that automates certain precise processes. The venerable Kingdom of Loathing uses "moxie" to much the same ends. Eternal Darkness splits mental/magical into two categories. Diablo begins with three playable characters, each based around strength, intelligence or agility; Phantasy Star Online reproduced the meme and split each class into three characters, divided among three races that related to each other as the classes did. In multiplayer games, a fourth entity sometimes appears in the form of the healer--most MMORPGs these days seem to be built around the interaction of a melee fighter, a non-specific ranger/thief support fighter, a healer and a nuker. Dungeons & Dragons, I'm told had the cleric before the rogue, but then, the cleric in D&D isn't much like the clerisy in any other RPG. And we're talking about three for now.
In RPGs that allow variable morality, it's generally a secondary stat, one that changes as a result of your decisions rather than leveling up. Arcanum uses a single good/bad axis, like the hilariously simple Jedi Knight and the highly confusing Darkwatch. Occasionally, these simple systems are used for things that aren't quite moral in nature, but function for the player much the same way, such as the professionalism meter in Reservoir Dogs or the trust bars in Splinter Cell: Double Agent. D&D did something a bit more complex by adding a lawful/chaotic axis perpendicular to the good/evil one, but its application in games is a bit odd, as it was really designed for tabletop games with actual humans improvising shit and then fighting about it.
So, what if we looked at morality instead as a primary stat, the heart that mediates between head and hands, the breath of life between the mind and the word...the spirit, the soul, that which is third? How would morality function as an ability stat?
There are a few options. As grace, favor of the gods, etc., morality could function as a luck stat. But a quick look at how the world functions shows this to be a fairly stupid and untenable idea. Besides, most good stories require at least a little bit of bad things happening to good people. Conversely, it could function as a kind of anti-luck, a demonic shit-magnet, but that would have to be offset with some positive to make it make sense. Protection from certain kinds of evil is a possibility, as is immunity to certain effects, such as fear or supernatural curses. Experience growth would be interesting, associating moral living with the life force. Virtue ethics might provide a useful template for ideas, as might the Christian cardinal/theological virtues. All of these, of course, hinge on free will.
So we borrow a page from Kant, and to some extent, Zoroaster, and associate the morality stat with free will. What does this mean? Well, first of all, it sets up morality as a matter of presence vs. absence; morality opposing amorality, not immorality. A character with a low morality stat is, functionally, an animal, operating largely on stimulus-response, i.e. the avatar spends some of its time on autopilot. This character pursues self-interest--its rationality is debatable, and might be linked with the mind stat--and thus might or might not be thought of as an egoist, but, y'know, moving on. At any rate, this sad avatar of low morals is ruled by avarice and fear. (An aside: I think lust ought to be here, but that's a very hypothetical area I'll not deal with in this post, because any game that purports to be about morality, sex, and violence is going to need--need--to deal with rape. And not superficially.) (S)he identifies all opposing players as enemies, and can't converse or exchange items with them. Teams and clans, therefore, cannot be joined; those of low morals are doomed to solo. This connects our oversimplified, somewhat childish, yet still kind of interesting morality signifier with the realm of the interpersonal. More to the point, it penalizes mindless (automated) aggression, and makes not doing things as important as doing them--more, since not doing things is effectively a reward for increased abilties. (This principle will need to be applied at a few layers, but, whatever.)
As for immorality, the perversion of substantive good, well, there's a couple of paths for that, fodder for future posts. In the meantime, what does the ruleset I've vaguely outlined above say? That the evil are fearsome, and more powerful individually than the good, but their power is limited and redounds upon itself by their lack of self-control. Finally, this ruleset would seem to give griefers their own class, although one wonders if they'd prefer to play as moral characters to as to fuck up other players more effectively.