Towards the end of Fear Effect on the PS1 there was the coolest scene. Unexpectedly the two remaining protagonist mercenaries, Hana and Glas, are pitted against one another because they have been tricked. They are literarily pointing guns at each others faces and I had to decide which one pulled the trigger . Its final, but either way, the survivor goes on to fight a different end boss and gets their own unique ending.
That was my biggest holy shit moment from a game. Having to choose like that because they are both really likable characters, Hana, the cool and calculating femme fatale, or Glas, the jaded yet honorable war veteran. They were also characters you play with through the whole game so I had an attachment to the two. I was totally like WTF. But I give props to the game developers. Ive never seen anything like it before or since.