The most disappointing moral choice system I've ever encountered in a game was the first Fable. Playing an evil character, I worked with bandits on quests, stole things and sold them to bandits, and was directly HIRED by bandits to do quests. With all of that, every bandit in the game would still attack me on sight. By defending myself, I received unavoidable "good" points. Secondarily, many main-quest-essential quests forced me to slaughter legions of "evil" enemies, netting me more and more good karma. I had to spend hours slaughtering innocent townsfolk just to get my alignment back to NEUTRAL.
Those situations are why I still think the only way to make a truly successful moral choice system is with factions. No universal "hero/villain" meter, just meters of how much particular groups like you. Fallout 2 made an attempt at this, and if that game hadn't been so horribly broken, I think it would have worked out pretty well. I don't play it, but from what I understand, WoW has a pretty well implemented faction system as well.
The reason no-one ever sees good moral choice systems is because the good ones aren't advertised as such - they're faction systems instead.