I like how Tactics Ogre had very different scenarios based on your decisions, and further developed your plot choices with exclusive side quests.

The Witcher was probably my favorite rendition of the classic CRPG multiple choice roleplaying, at least for the first half of the game.

I also appreciate how FFVII's choices, while not affecting the game, did change your perception of Cloud, given the ambiguity of the script. He wasn't necessarily emo.