To be frank more than I care to mention but here's the short list:
Final Fantasy 4, 5, 6, 7, 8, 9, 10 and 10-2
Persona 3 & 4
Digital Devil Saga
Metal Gear Solid - all
Shadow of the Colossus
Prince of Persia - Sands of Time
The Void
Vampire the Masqurade - Bloodlines
Red Dead Redemption
Way of the Samurai 2 & 3
Grandia 2
Suikoden 1, 2, 4, 5 & (somwhat) Tierkis (never played 3)
Dragon Age Origins
Mass Effect
KotOR 1 & 2
Fallout New Vegas (a little)
Wanko to Kurasou
Saya no Uta
Those are about all I can think of at this precise moment though there are probebly more.
But more than any other game in my library Okami has moved me the most, I can't even think about that games ending without bursting in to tears.