Well, if someone study psychology, feel free to add and correct. I just make some trivial assumptions… Let's assume the egoism as an inner driving force for a character. There are no evil, only different opinions for problem solutions. Then let’s portray the ways of the egoism. Like when one put his desires higher then human's live... Of course it's not clearly that evil - the character just using all the possibilities for his own purpose. Then maybe for other character - egoism is when he suffers the pain for innocent people... It's just feeding his ego, granting him a feel of being a hero and a martyr.
But there is no place for tracing character “alignment” in such system, because the designers can't be sure of the motives for his choices. As in real life - donating to the poor is perceived as good, no matter what the motives were - altruism, ego feeding or just a desire to be perceived as good man. So the game world must judge actions first. Of course some game factions may see it in different sides, so that is why overall good/evil meter is useless. If my character see Gizmo as more powerful force of survival for a Junktown, and he perceives survival of mankind as the greatest goal - his intentions just cause approval from some people and disapproval from others. There is no greater evil in that.
I think player motives may be taken into consideration by outer driving forces – like philosophies, or religions. Like Sigil factions maybe. The Paladin of Righteous feeds his ego by acting goody and knightly, when the Free Ranger sees freedom from tyrannical knights as a main goal. It creates some nice connection of the character and the game world. And then some time the character may understand that, omg, his faction being wrong and take another philosophy. Maybe it’s his own philosophy.