im going for spec ops: the line

It was, and sad at the end for him but it had to happen.

Off the top of my head, the end of Paper Mario: The Thousand Year Door. It's totally silly, because it's a colorful game with silly little sprites, but something about that last boss battle was really uplifting and touching to me. In fact I might even say that I was more moved BECAUSE it was done with sprites. I find I connect more emotionally with cartoons/puppetry/etc. than with real actors or realistic cutscenes. Maybe it's something about the innocence, I don't know.

Go easy on me, I was a kid... I cried at the end of Kingdom Hearts 1.

i totally forgot about vivi's innocence and how everything ends for him, sad indeed

The whole of Persona 4 Golden, nothing quite like living out a whole year of someone's life.

Skyward Sword and Shadow of the Colossus.

Persona 4 and Brothers.

So much this. I don't think there's quite the experience like the ending of T&T. Such a swirl of emotions from that one. 

Pokemon Mystery Dungeon 2. I played it when I was pretty young but it still gets me in the feels at the end. For a more mature title I'd go with Persona 3 because dat ending.