The ending of Conker's Bad Fur Day wasn't a Tear Jerker personally, but it has very high potential in that respect... if for no other reason than because you don't see it coming. Conker: "It's true what they say, the grass is always greener. And you don't really know what it is you have, until it's gone... gone... gone."
Logged: The commanding officer is aboard. XO Pressley stands relieved.
The ending to Lufia II. At the time, I hadn't played the first game at all, so I didn't know that Maxim and Selan die at the end of the prequel. The way it played out though, I doubt having that foreknowledge would've softened the Player Megaton Punch at all, and the ending theme just makes it that much more tearjerking. To date, more than twelve years after seeing that for the first time (...great, now I feel old too), I still can't sit through the entire ending without bawling like a fucking child.
There needs to be a word for those brief moments of clarity where you realize just how profoundly weird your life is.
That one scene in Lost Odyssey, anyone's who played it would know exactly what I'm talking about, though admittedly Mack's big no was pretty narmy. But Cooke's reaction was what made the tearjerker.
Oh, and the story with the letters and racist village. That was pretty messed up, and like the one time where Kaim was flat out wrong.