See Photo for mind map.
My favorite emergent narrative game has always been Sid Meier’s Civilization.
In terms of embedded narratives, I absolutely loved the story of L.A Noire.
As a kid I played Lego Star Wars video games purely for the evocative nature of bringing me back into the world of Star Wars and the awesome characters.
Finally, I’ve used it for a few examples but Assassins Creed was my favorite story. Such a great narrative that blends into character choice and action.