As much as i dislike that lil psycho sphere, jesus christ is Emil's Ending traumatic, i mean jesus ****ing wept i felt bad for him, i constantly *****ed about how ****ty he was and there he was with retrograde amnesia cuz he duplicated himself to save the world and the poor sod can't even remember his friends who inspired him to become like this.
I think the ending where you get to either join the machines on their ark or stay behind is gut wrenching in way, 9S is literally given the option to leave all behind him and ascend the mortal plane (for androids) and lose all he loved or stay behind and die.
{edit} nah you know what was way more emotional, Pascals ending. That poor poor sod tried so damned hard to make things better for his village and it all screwed up. The children couldn't handle their fear and so he leaves it up to you to decide his fate. If you let him live you can buy the childrens parts from him.