Hm.
I though games like Planescape Torment, Arcanum and Vampire: The Masquerade - Bloodlines handled morality pretty good. Particularly VTMB stands out for me. It's not without faults, but from a narrative perspective it did things really well.
Because your character was not very significant in the big schemes, just someone manipulated to believe one or another thing; because there was no one big truth, just many different perspectives the whole morality system was opened up. What you did had consequences, but there was no real clear answer to right/wrong.
Of course Bloodlines paid for that by being largely linear. A strong narration limits character choices. Many character choices limit narration (as with each choice narration becomes more complicated). That is what the more black and white morality tries to achieve, really - abstracting a concept, and making design easier.