The game I have actually finished recently is inFamous, a superhero sandbox game. Generally a lot of fun, but sort of short and some parts of the city design stretched my disbelief an awful lot, especially the el tracks that only circle a few square blocks. The most obnoxious thing about the game was probably the ending, which pulled a really stupid trick that made me want to turn a fire hose on the main villain.
One of the most important aspects of the game is it's "moral choice" system, where you have to decide through a series of major story choices and minor actions whether you want to be a good guy or a bad one(and since the most powerful powers are only available to those at either end of the spectrum, you can't sit in the middle). Some of these are actually fairly well done: the first choice is whether or not to share food in an urban ghetto with other starving survivors, or zap them and make sure that you get it all for yourself, and that makes perfect sense within the context of the game. However, there are some that are extremely obnoxious. The most banal of these was one where in the course of doing something else a random street artist stops you to ask which one of the two posters he's made you like. I ended up picking the one that was bright red and looked like a warning sign, despite knowing that was the "bad" choice. Why? Because I had noticed that it was actually often bad for the welfare of the random civilians to come up and take pictures of me if one of the gangs in the area suddenly decided to open up, especially if they brought heavy ordinance. Basically, being around me was dangerous and people should stay: an excellent rationale for a "good guy".
Perhaps the most direct choice in the game is when the villain makes you choose between saving the hero's girlfriend or six unnamed doctors. Now, I've passed villainy 102, and I figured out immediately that if the villain was determined to kill the hero's love interest, then there really was no choice, except maybe whether or not the doctors would die. I picked the six and sure enough, that was the "good" choice. After that, I went and read the plot synopsis on wikipedia, and sure enough, there is no choice. I read some more of that, and figured out that some of the most important choices really don't matter, besides producing slightly different cut scenes depending on whether you choose good or evil: the plot has only two parallel tracks it can run on.
By contrast, a game I've been playing for a while, Valkyria Chronicles, presents one of the most unusual reactions to a wartime action I think I've ever seen in a game. The enemy has this magical super soldier that is tearing up your army, and the hero's best friend figures out that his side can have one, but he has to wound the hero's love interest to get it. Well, he does just that...and at least so far, the game almost completely condemns his actions(I haven't finished it yet, some of the final missions are obnoxiously difficult). He saves hundreds if not thousands of his own soldiers and it leads to a major victory(and he doesn't actually kill anyone!), and not just the hero, but the authorities in general seem to think that he belongs in jail. It's...well, the game itself is often overly sappy and idealistic, but that was the part where I was exclaiming at the TV about the stupidity.
I've just started playing Fallout 3, and so far the conversation choices presented in that game aren't exactly wowing me with their originality. It seems extremely odd to me that a character that has been a day or two out of the vault would have their "neutral option" often be asking for money in some way: that even in the first town many of the responses seem like they would fit an experienced wasteland survivor, not a 19 year old kid seeing the sun for the first time.