The problem with so-called morality in games is that its a numerical value depending on you following its parameters to end up either good or evil. And, to be honest, Morality should effect the gameplay more in RPGs, especially games with alot of the "pick what line to say" gameplay, by eiter restricting you from being at 100%evil and then try and change it by being Jesus for 3 quests.. Maybe force you to work your way towards neutral.
Morality is about more than different endings, its about reflecting the person, if a person does not define stealing to be evil but a "nessecary action to stay alive", it shouldn't make him more "evil". Most games gives you X points of evil for stealing an item, but at some point it should stop, because it becomes normal to the charater.
Initial rant over, sorry about that.
Best game have to be.... cant think of any.
Best morality system, World of Darkness' (a pen and paper roleplaying game) is what I would define as close to perfect. Depending on what sin to morality you commit, you roll a number of dices, depending on the roll, either your charater comes to terms with his actions (loses a point of morality, not really caring about what he just did) OR your charater feels sorry for the people he hurt, and try to attone for his sins, or justify them in some way (mass murder CAN be justified by a sick mind) and as your morality drops, lesser sins wont call for a roll, as they are associated with higher levels of morality.. A great concept, as most games have the "you stole a cookie!" and takes you 3 points further into evil.. No matter how evil you already are. I mean, in Fallout3 you could nuke a whole town full of people, just to make some rich guy have a "lovely view" from his tower, and still get hit by the bad/evil stick for stealing a stake..
But well, games are getting there, slowly and steadily.
Ow and I thought of a good morality system.. Neverwinter nights 2.