I would have put in metro last light on my list, but they locked the cannon ending behind the moral system, after two playthroughs that failed to get that ending, I can safely say 'fuck that'
So here's what I have instead.
Deus Ex. The ending is a huge interconnected level, and you choose your ending by doing a bunch of tasks spread all over it while the antagonist mocks you, and then protests, and then begs you to stop as you go about your business. Great design and setup. 
Mafia 3 also had a great ending. A perfect last level, followed by some great denouement scenes and choices that properly respected your decisions across the course of the game. Basically the complete opposite of Mass Effect 3's ending, which I experienced for the first time a couple months ago. I was so frustrated by how slow and dumb it was being that when I finally got the ability to move and choose an ending, I shot at the ghost-child-avatar thing, and instantly got a bad ending. Reloading took me back over an hour and a half of unskippable bullshit, so I never even bothered trying again for a real ending, because I was so fed up with it.
obviously MGS3 Boss: The End.
Either let him die of old age
or snipe him in a wheelchair before the actual fight.
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