We're here... top 5. Of the final five moments, four are scripted, one is nostalgic. Three of the four scripted events are pretty widely regarded as some of the best moments in gaming history. This is the fourth, a moment that I would consider one of the most underrated in gaming.
I just discussed Metal Gear Solid 3 over the weekend. Let's hear a bit more about the ending...
The Shagohod has been destroyed.
Volgin has been killed.
The mirofilm has been retrieved.
The mission is successful - except for one last detail.
There's just that matter of the traitor - The Boss. She'd been Snake's mentor and mother figure, and even as she defected, she seemed to be a sort of semi-malevolent guardian angel. You trudge through the swamps and woods of the game, backtracking to the pickup zone, knowing all along she's waiting for you there.
Sure enough, there's one last fight. The fight itself is gorgeously presented (a field of white flowers, with scattered petals blowing in the wind) and challenging (you're only allowed to use CQC moves, and you're fighting the woman who taught all of them to you).
Eventually, you gain the upper hand and the woman who may as well be your mother is lying on the ground, beaten, but still alive - but you know what the game is going to force you to do.
There's no cutscene, there's no aiming, no quicktime event. The game just sits there and patiently waits for you to fire that final shot (the last action you're allowed/forced to make in the game before the final cutscenes).
The white flowers all instantly turn red. Sure it's an overly stylish bit of melodrama in a series that already is fairly well known for such things, but in context, it's absolutely gutting.