The Demon Path is about the last place you might expect this, but if you lose the last battle of said path, you get the 'good' ending where Gig recovers from his brainwashing and returns to his duties as a Master of Death. The heroes seal Revya into the now empty Onyx Blade. Inside, your character meets... Danette, who decided to join your character, not wanting you to suffer alone despite everything you did, and then sings your character to sleep using a lullaby your character would sing to her when they were kids.
Thorndyke and Penn reuniting after he thought Penn died when he was just a toddler. Also counts as a Tear Jerker. Penn showing that he's more mature than you think when he decides not to live with his dad because he didn't want to ruin his little brother's future and he was happy with the Nereids... Just plain touching.
The Levin ending. Either gender is considered one, but female Revya's Levin ending deserves special mention, especially when she sees a pretty flower and Levin tries to say that it's nowhere near as pretty as her, but can't exactly get the words out. Awwwww...