The main series and Mystery Dungeon series Pokemon games are really emotional for me, and there is no lack of content in them I find incredibly moving and that gives me a lump in the throat and tears in my eyes, but as long as I don't have to speak out loud, I can usually keep the actual crying in.
The scene in Pokémon Mystery Dungeon: Explorers of Sky where my partner Pokemon is crying on the beach made me cry.
It didn't help that I named my character after me and the partner after my turtle who had just died, and seeing "her" lie on the beach crying for "me" made it even more emotional than it would have been otherwise.
Apparently some people thought Lavender Town was creepy when they first played Blue/Red/Yellow. I just found it saddening. Reminding me of losses of dear pets.