Either Jade Empire or Fable 2.
With Jade Empire, there is no 'good' or 'evil', just the Ways of the Open Palm and Closed Fist. Do you help people out of good will, or so you have a little extra money? Do you kill someone to help the world, or so you can nick the key to their treasure trove? It's not the best description, but the Open Palm represents Harmony (affinity with all life, live for the sake of others) and the Closed Fist represents Discord (Honour above all, corrupt), but they are used in such an innovative way that you would be surprised.
As for Fable 2, it used a 4-way system with it morality: Good/Evil, and Purity/Corruption. It needs a bit of work, but it was a serious step up from the standard 2 way morality systems used in most games.