I think the most emotional moment had to be
Isara's death in Valkyria Chronicles and then later when Rosie sings that song I actually did cry.
Otherwise Shadow of the Colossus the whole game was emotional between killing these Colossi that don't seem to be doing anything wrong other then living and watching those sad eyes as you kill them is always emotional.
There are more but these two stand out in my mind.
Isara's death in Valkyria Chronicles and then later when Rosie sings that song I actually did cry.
Otherwise Shadow of the Colossus the whole game was emotional between killing these Colossi that don't seem to be doing anything wrong other then living and watching those sad eyes as you kill them is always emotional.
There are more but these two stand out in my mind.