All of them. I'm so emotional.
More specifically, Xenosaga Ep. I and III
Final Fantasy VIII
Final Fantasy IX
Final Fantasy X
Dark Cloud (seriously beginning of the game, first level, when everything is destroyed, I'm just ;_______________; until I get at least half of the stuff back)
Dark Cloud 2
Majora's Mask
Ocarina of Time
Others that I can't think of right now, but there are more.