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Tear Jerker: Final Fantasy III
The scene accompanied by "Elia: Maiden of Water". Better tears, happy tears (or, well, sad since the journey is over) likely accompany the post-game sequence (in the DS version, at least).
After getting the Earth Crystal jobs, the party decides to pay a visit to their good old friends and mentors, Doga and Unei. When they arrive, Doga and Unei immediately challenge them to fight to the death. Luneth, Arc, Refia, and Ingus are all horrified at the notion and refuse to do such a terrible thing. The old mages simply tell the kids that if they refuse, they'll be killed. The boss battle with them is one of the toughest in the game as you're forced to first kill Doga and then Unei without so much as a breather. They really are sincere about killing the Warriors of Light if they hold back because if they can't, they have no hope against the enemies to come. After that nobody comes out and says My God, What Have I Done?, but you can see it on the kids' faces as Doga and Unei go on to declare which light of virtue each holds before dying.
If you return to Doga's house after his death, you will find all of his servant moogles mourning his death. It's made even worse by the fact that YOU killed him.
As though the above with Doga and Unei wasn't bad enough, they make another Heroic Sacrifice for the party by expending the energy of their souls, resigning themselves to Cessation of Existence. Bear in mind that Doga and Unei had told the kids not to mourn because their spirits would remain. So much for that consolation.
Xande's Start of Darkness. You've spent your immortal life apprenticed to a master wizard - no doubt making close friends with the other two apprentices, by the way - and what is your reward for this dedication? One gets phenomenal cosmic powers and an entire continent, the other becomes the ruler of the world of dreams, and you get... mortality. And they call you evil when you want to keep things the way they were? Xande got painted into the villain corner, plain and simple.
Basically, Doga and Unei outright killed him, though not before they essentially arranged for their deaths. What's Xande going to think when/if he finds that, essentially, Doga and Unei enviedhismortality?
King Gorn's death. For weeks, he's been mind-controlled by his Evil Chancellor to set his soldiers against each other and to banish his ten-year-old son Alus from the castle. And the final act in Gigameth's plan? Have Gorn murder Alus in his bed—but the order is too much, and Gorn turns the knife on himself to save his son.
The whole "Boundless Ocean" sequence. First, you see a world that is shrouded in a strange, swirling ocean of darkness, with only two small pieces of land uncovered, accompanied by lovely but haunting overworld music. The kids save a young water priestess named Aria, who is sweetness incarnate and becomes particularly close to Luneth as they go to restore the Water Crystal. Just before they can, the Kraken fires an arrow at Luneth and Aria intercepts it. The arrow turns out to have been poisoned, and after the party is done killing Kraken it's too late to save her—she dies in Luneth's arms. Worse, they have no time to mourn, because the removal of the dark ocean starts a quake inside the cavern, forcing everyone to flee and leave her body there.