Far Cry 3: A lot of Alice in Wonderland references and the human moral compass is thrown for a loop.
Final Fantasy VII: Story had me wrapped around it's finger, thinking about it gives me chills to this day.
Assassins Creed: the Assassin/Templar war is very in-depth and the animus idea is pretty insane.
Minecraft: No explanation needed.
All I've ever heard is that Far Cry 3's story is terrible and messy. Anyone care to weigh in on this?