This is a hard choice. I'm really tempted to go Persona 3 (Though Devil Survivor 1 and 2 and Persona 4 give it a good run for it's money for best ending of any SMT game I played), but I am going with Mana Khemia: Alchemists of Al Revis. A few different endings, no matter which one you go with I still stand by this. It may be the most emotionally involving fight in any RPG, and I can't explain why at all without ruining it.