It's a tough decision, but I'd have to say KHII. Both are very emotional, but I think it's harder to have a happy ending make the player cry than a sad ending, and judging from people's reactions, KHII did just that.
For me, I was torn between laughter and tears as I watched the second ending. That a game could make so much happiness bubble up in my chest...that's impressive. Not only that, but while the first game's ending had that blatant "the story's not over yet" vibe to it, the second ending was possibly even more impressive: the story could very well be over for these characters, and I wouldn't mind if it were. They truly earned their final happiness, and I think that makes all of us happy.