The scene when Dorne becomes stone. Just everything about the scene is sad - him asking to lay on his own bed, and giving the little music box to the girl he loves, Millie, seconds before turning into stone...
Poor Pericci. Her ending shows her all alone, like she was in the beginning since she couldn't stay in the future with Roddick and Millie. With just her Ocarina.
Phia's ending, if you didn't recruit Cyuss or Ashlay. She's wandering around Mt Metorx, implying that her name hasn't been cleared, and missing Roddick quite badly too.
When you discover Erys' body when you have both Ioshua and Mavelle in the party and Mavelle reveals that she's Erys controlling another body, and the guilt of what she did while she was Brainwashed and Crazy leaves her Driven to Suicide, and thus Ioshua finally gets reunited with his sister just to watch her die. In the remake you can keep her from doing this and instead return her to her true body if you also have Ashlay in the party.
Durss is a small village that had been through numerous monster attacks in the past, leaving very little residents left and a lot of abandoned houses. It later gets completely destroyed by Asmodeus after the party collects all Emblems, and it's also implied that none of the remaining residents survived or evacuated due to how unexpected the attack was.
Made even worse if you did the PA in the village where Roddick and Millie (plus Pericci, if you recruited her) help a little girl build lots of snowmen, prior to Asmodeus' attack.
