It seems that any game coming out these days touts "moral ambiguity" as a selling point. Plastered all over the advertising of Bioware's upcoming RPG Dragon Age: Origins, for example, is reference to the game's "complex moral choices." It remains to be seen whether or not the implementation here will be different than recent releases, but I usually find the concept of "moral ambiguity" to be pretty meh in practice.
When put into play, morality in video games tends to fall into two very distinct camps: an action has two very clear options, either the stereotypical good choice or the stereotypical bad one. The way these choices are presented usually have no ambiguity whatsoever– it's obvious which is the "good" decision and which is the "bad." Bioshock has been heavily praised for these, but the only moral decision you make the entire course of the game is whether or not you use the looks-like-children-but-aren't-really-children Little Sisters as a resource to improve your combat viability. While the game gives you a frowny-face ending if you harvest all the Little Sisters, it ultimately has no effect on the game whatsoever.
Fallout 3 was another recent title that portrayed this as a feature of the game. While the choices you made as you progressed through the game weren't limited to a single decision, they were just as irrelevant to your overall progression whether you went the good or evil route. One quest chain in particular, the Roy Phillips/Tenpenny Tower quest, was such a glaring example of this irrelevancy that the first time I went through it I actually thought my game had bugged out and defaulted me to the evil outcome accidentally. There is a superficial implementation of "punishment" in Fallout 3 whether your karma sways too far in either direction, but you get an equally strong faction coming after you regardless of your character's constitution.
Sometimes "morality" is irrelevant, but other times it's outright ridiculous. As you play through Fable you're given moral choices but as the overall goal of the game is to stop a Super Bad Guy, it starts to raise the question of why a heroic asshole is doing all these "good" things. At one point you're given a choice between sparing or killing your rival at ye olde hero school, but it doesn't matter which route you choose. If you spare her you get a golf clap, but she doesn't do anything for you to any tangible degree for the rest of the game. Similarly, you can kill her, but you don't get kicked out of the heroes guild for doing it.
It's pretty obvious why moral choices are put together so badly in games– it would be a lot of work to do well. To say nothing of the programming challenges with implementing so many branching options, the writing itself would be monumentally complicated to account for. It's also a challenge of creating an overall plot that makes sense whether you play good or evil; why would an evil character have a vested interest in stopping the big bad demonic half-god the same way the good player is, after all? Still, when the usual implementation is so half-assed I often just wish developers didn't even bother. I'd rather a linear progression than the presentation of superficial morality that has no effect on the game itself. It would be interesting for an RPG to let you play as an evil badass, but actually penalizes you for doing it: if the over-arcing goal of the game is to defeat a big bad evil, maybe if you begin to resemble too much of what you're fighting, other morally-good characters will stop having anything to do with you for the duration of the game, leaving you more on your own to come up with solutions. Similarly, perhaps there's some sort of super weapon that you can destroy or utilize, and the good character who tosses it away has a tougher time of things because of that choice. Games seem to want to ensure that the experience is the same whether you play good or evil and seem afraid to punish someone for going one way or the other– but why provide a choice if the choice is meaningless?
I do have high hopes for Dragon Age: Origins, though. Bioware is often championed for their nuanced storylines and well-thought out plots, and Mass Effect had one of the better "morality" implementations that I've seen. People in real life are typically not stereotypically one-sided archetypes of light and darkness; we're all grey, and it would be nice to see games that start to take advantage of that reality and have the bravery to provide repercussions for people who go to either side of the good/bad spectrum.