There's a young couple living in Clock Town. One of them, Kafei, has been cursed to be a child and a mask of his was stolen (it's usual for marrying couples to exchange masks you see). You spend three days helping Kafei, who's in hiding, and convincing his fiance Anju to stay (the world is ending so her mother is telling her to leave and forget Kafei). If you decide to do it, you can help Kafei and Anju by getting Kafei his mask. He then runs back to Clock Town to marry Anju, who will be waiting for him. It was their promise to be married on the night of the Carnival of Time you see.

So you stand with Anju and wait for Kafei. And you wait for Kafei. And he doesn't show up, until just a few minutes before the world is about to end. They marry, and promise to await the sunrise together. They don't care about the end of the world, they just have each other.

MY FUCKING EYES ARE TEARING UP, DAMMIT.

Oh man I forgot the ending to Bastion...

Not the ENDING ending, but the part leading up to the ending after your first choice. I chose the "good" option and.... it made me teary eyed. I was like "No other game I can think of has this IMPACT". Majora's Mask maybe, but that was pretty intense.

I've got a tear jerked out of me in a couple games but one of the moments that hit me the most was in Final Fantasy 4.

You have just beat one of the elemental archfiends and were leaving the castle but you sadly fall into a trap. As you walk into a hallway you hear the archfiend talk saying you will join him in the underworld. At that moment the walls begin to close in on you and your party. You can't get out because both doors are locked, the situation seems hopeless. That is when the two small children in your party (who were mages in training) step up and look at each other. The party wonders what they are up to as they soon start to say goodbye and thank everyone. As the walls get closer they cast break on themselves to turn to stone and stop the walls. Sad music begins to play as the sage in the party does his best to cast esuna on the twins, but it sadly has no effect since they became stone willingly. That's when the party swears to the twins that they will get revenge on the man responsible and head off to their airship.