Soooo...what do you want/expect from a morality system? Okay, you don't want to be a total saint/demon all the time. Do you want a little rainbow sticker when you rescue someone's cat from a tree? Face it, the majority of moral situations don't have any lasting effect at all. I mean... Planescape: Torment kind of worked here, because there were sort of some good middle-of-the-road solutions. But in Planescape, as in many games, mostly it's an issue of good vs. bastard vs. apathy (which is strangely enough how it works in the real world!).
Ooh--Here's a good one for you though. Valkyrie Profile. That might actually be a REALLY GOOD example of an RPG for you guys, what do you think? For the uninitiated: You're roleplaying as a valkyrie who is sent to collect the souls of recently-dead heroes and send them up to fight in Ragnarok, but first you have to train them a bit (IE level them up). You can make a big deal out of giving Valhalla exactly what it wants--as many heroes as it can, your best-trained ones, crippling yourself in the process to fight the good fight--or you can slouch by, barely accomplishing your objectives, to keep kicking ass on Earth. Also, Odin demands that you send him all the cool artifacts you find--but you can choose to disobey him and keep them instead, at the loss of some favor.
Unless you *really* screw it up, doing 'good' doesn't have a huge game impact. It's actually kind of hard to lose Ragnarok if you are remotely doing your job. But I guess that's where roleplaying comes in--I mean, it's my job to obey Odin, and the game is going to make a point of my disobeyal if I don't, so I feel compelled as a player to do the "right thing". Isn't that roleplaying? Isn't that morality? Deciding when to make sacrifices for *no* personal gain whatsoever? It's hard to put that into a game.
Iji does the same thing from a morality perspective, too. Sure you can play it kicking all sorts of ass, but it's possible to play it as a pacifist and feel *really bad* when you kill someone. Your life is more difficult if you avoid killing (except for a super-weapon at the end if you did perfectly; who cares) but you, the player, get into that role. So, uh... I guess Valkyrie Profile and Iji are good examples of game morality to me. And Iji isn't even an RPG (not really).