The moments that stood out to this troper were that scene with Lavitz in Mayfil (although, strangely, his actual death didn't make this troper cry), the ending (especially the short little scene right after the credits) and finally, the scene in Aglis, where Savan dies and so do all the magical creatures he created.This troper doesn't remember exactly what Ruff said, but whatever it was, it made her heart break.
He said "it's rough, Ruff."
Another scene worth mentioning is when Dart and Lavitz enter the ruined fortress in the swamps: inside, they discover that the Green Dragon's poisonous breath has killed both the attackers and the defenders. As unbelievably saddening music plays, Dart says "In death, there are no allies or enemies. Rest in peace."
Rose's flashback to the final battle of the Dragon Campaign, especially the scene when Belzac gets fatally impaled by a Virage while trying to save Shirley from being crushed by falling rubble. And after all that, Shirley refuses to leave Belzac's side and dies along with him...
In the same cutscene, Rose trying and failing to reach Zieg before the curse of petrification overcomes him.
The sheer amount of Alas, Poor Villain in Legend of Dragoon never fails to sadden this troper- particularly Emperor Doel's death scene, in which the Evil Overlord faces death with such dignity that the heroes actually salute him as he vanishes into energy.
Also Lenus death is really sad, considering she's dying for a man who doesn't care for her.