I generally prefer choices that ill dramatically change the story. By which I mean it moves the plot into an alternate path, not simply change the flavor of the NPC text. Things like choosing to help cure Kid's illness in Chrono Cross or choosing whether to participate in the Balamusa Massacre in Tactics Ogre are far more engaging to me than choosing either an alternate route or text that only changes the scenario on a surface level.

As of right now, the Massacre scenario from Tactics Ogre is one of my favorites because it really changes the dynamics of the story and characters. Not to mention the Law path I'm taking paints the MC in a way you don't really see too often in the medium.