Delixe: You can rule out BioWare games. They either follow the D&D alignment system like Baldur's Gate or the good/evil system seen in KOTOR and Mass Effect. Dragon Age: Origins was unusual in that respect as there was no alignment, choices just mattered to your companions.
Fallout: New Vegas has an interesting system. It has Karma but it doesn't really have an effect. Factions treat you how you treat them so you can be the most evil bastard in the wasteland but as long as you were helpful to the NCR (for example) they were Bro's.
On the contrary any D&D based alignment system is going to give you one of the most complex and variable morality *systems* out there.
Planescape however does this much better than the Bio games. The D&D alignment mechanic is the same, writing and characterization are just more subtle and nuanced in PST.
Hell the D&D alignment system is what the 'chaos/lawful nonevil' stuff the OP was talking about in Ogre Battle was lifted from.
In general though I'm getting a bit fed up with morality systems as such. Black/white morality has always been asinine, and if you're shooting for moral complexity and gray areas better to actually write characters that way and provide murky, believable choices for the player.
