Metal Gear Solid 3... Final battle and aftermath, when he goes up through the long ladder
Metal Gear Solid 1... The ending theme/video
Silent hill, the Laura cutscene (if youve played it, you know what i mean)
The last of us... prologue.
Shadow of the colossus... the ending
Thats at least the games that i remember, and even as they havent brought me to tears , they actually moved me close to it.

Kingdom Hearts 358/2 Days and Birth by Sleep.

Crisis Core: FF7.

Ive never cried I think, but have come close a few times. Only one I remember right now is The Last Of Us.

Ocarina of Time

Tears of joy at first then tears of sorrow when the game has to end

This, dat (supposed) ending.

Also Pokémon X/Y was really emotional aswell, I got the game early and I rember finishing it just a few hours before Flolette's backstory was leaked online, I shed a tear after seeing again some of those images

None.

Thief 2, Mafia 2, Deus Ex Human Revolution, Commandos 2, Hidden&Dangerous 2 - they were huge disappointments for me and made me cry inside.

R-Type 2's difficulty made me cry.

This exactly.

I really can't remember from older games I played, but end of Zelda Skyward Sword was pretty emotional for me.