Professor Layton and the Unwound Future, Professor Layton and the Miracle Mask, Professor Layton and the Azran Legacy, Professor Layton and the Last Specter. All of those, I played from 4th grade to 7th grade. Cried at every ending.
also Halo 3(badass quote when Arbiter kills Truth), Halo Reach(Carter's death), Halo 4(Cortana death). I cried when I played these with my sister years after i first played them. I'm a social cryer, or maybe crying is contagious. I cried at a few scenes in CoD, umm I think Blops2 and Advanced Warfare also watching my sister play them.
I tried to make myself cry at the end of SOMA, because it's so hopeful, but I just couldn't. I finished it today. I like when games can make me cry, but i have to force myself to be invested in their characters.