While I don't play as many role-playing games as my pear-shaped counterpart, I've noticed a pervasive trend in her games where the player is forced to make a decision that will upset the very balance of good-and-evil in the game's universe depending on the choice the player makes. This choice typically boils down to selecting between two clean-cut dialogue options or actions; buying a seasonal gift for the crippled boy with the funny accent is Good, while torching his village and laughing as he awkwardly hobbles away is Bad.
I don't mind this perceived open-endedness – it makes the game's plot seem less on-rails, even if it sometimes just forks into two paths of equal length – but it seems like developers keep trying to make the moral choices exceptionally "game-y" by linking them to a slider that arbitrarily shifts between More Good and Less Good. I'm sure this is easier from a design perspective: the plot can fork based on the world's general perception of a character, rather than having the world specifically reference the player's various Good and Bad actions. But it leads to an unintended gameplay mechanic where "morality" becomes another meaningless stat for the player to level up, or down.
Because I have some personal experience with it, I'll loosely use Fallout 3 as an example here. If I pick some guy's lock, my Karma takes a small hit. If I pick several hundred locks, my Karma plummets until I become The Dreaded Baron Phenoix, Picker Of Locks, feared across the lands for my lock-picking ways, and I'll even get a shout-out from the Galaxy News Radio DJ, Three-Dog, about how dreadfully feared I am. However, if I then give some bottled water to a beggar a thousand times, I'm a Paragon Of All That Is Good again and I can venture into a distant town and walk the old lady across the street. Picking all of John Q. Owns-A-House's locks should put me on bad terms with John Q., and rightly so, and I wouldn't find it unfair if John Q. subsequently packed up his locks and skipped town before I could do him any favors. But I would think I could pick every lock in town and still maintain a moral high-ground over someone who dropped a bomb on it.
As far as moral choices in dialog options goes, in Fallout 3, it usually works out like this: if you ask to be paid, you're a bad person. As a result, during my Good Guy run, I did everything everyone asked and refused their rewards at every turn, not because I'd "feel bad" if I asked for compensation, but because I didn't want my Karma to go down. Conversely, on my Bad Guy run, I still did everything everyone asked, but made sure to ask for a hearty reward for my efforts.
Fallout 3 almost does a few things right. For example, it's possible to put a bullet in Three-Dog's head. This isn't the result of a dialogue tree nor is it guided by some sort of prompt, the game simply puts the player in a situation where one is armed and in the same room as Three-Dog. Killing him actually effects the world: he'll no longer DJ GNR and his plot missions and sidequests will be inaccessable. However, this causes other characters to be annoyed with you at worst, and at best indifferent toward you after you've satiated that thirsty beggar a few times.
Maybe on my next playthrough I'll just rummage through Three-Dog's stuff and steal his wallet. That'll show him.