Early on, the child hero and Bianca go ghost hunting at Uptaten Towers. They get captured and a bunch of skeletons are going to cook them. One of them refuses, and the other's threaten him that the "scythe of Hell" will reap him if he doesn't. If you go back to the kitchen after this, you'll see that the one who felt bad became a human soul again; so he'll go to a peaceful afterlife with the other good ghosts after the heroes clear the stage.
The wedding scenes, no matter which bride you pick.
The hero's daughter asking her dad to hold her hand when it's dark or high up.
Meeting Bianca again after all those years.
The reunion with his wife after being separated by ten years of being Taken for Granite.
If you're taking Parry with you at that time and you Party Chat just afterwards, you'll see the normally talkative Kid Hero spurting "Mom...! Mom...!", at a loss for words and probably holding back tears.
Returning to your Doomed Hometown and finding it restored to life as if it had never changed.