After pointing out some glaring flaws in the way choice and consequence is handled in Fable and Mass Effect, That Gaming Site briefly covers one game that managed to get it right: Troika's Vampire: The Masquerade - Bloodlines.
Vampire: The Masquerade - Bloodlines is a lesser known cult hit with some of the best writing I've encountered in a video game. The best part comes at the end, where players will find a genuine split path. The amount of paths you can choose from depends on which NPCs you decided to be nice to and how well you did in certain quests. As a bonus, none of the groups that you can side with are clearly good or evil. Technically there are five possible paths to choose from, although each requires you to either kill one powerful vampire, kill a different powerful vampire, or kill both powerful vampires. There are then five endings, although three of them are very similar, leaving players with three distinct endings. One of those endings may feel like a game over ending, but the other two are equally satisfying and hilarious.
Bloodlines contains all of the elements, although primitive, of a true and realistic choice-consequence system. You go through the game without knowing which characters are good and which choices will benefit you most. Your choices and performance affect the amount of paths you get to choose from later. Most of these paths lead to different final missions and equally satisfying endings. An even better game would have more of these paths, and have the path split show up earlier in the game. But this would require extra effort and money on the part of the developers, which reduces the chances of the future existence of such a game considerably. As a depressing side note, the developer of Bloodlines, Troika Games, went out of business almost the moment the game was finished.