Chrono Cross/Tear Jerker

• Kid's reaction after Serge helps her out of Lucca's burning orphanage and they watch the scene from afar. That Serge vanishes very shortly after Kid laments that she will be left all on her own doesn't help much. Not to mention the implied fates of the Trigger crew, Kid's reading of Lucca's letter, and a number of subplots and character backstories. This can be a depressing game.
• The fight with Miguel, and the events leading up to it, especially with the music that accompanies it.
• The ending, where Kidd sadly declares that she'll always search for Serge. The music just makes that scene.
• If, on a New Game+, you defeat the Time Devourer before assaulting Terra Tower, then the Dragon God joins forces with the demi-humans and slaughters the humans of El Nido.