Seliph's conversation with the ghost of his parents after killing Arvis, especially with the remixed version of Sigurd's theme.
Claude's conversation with Sylvia in chapter 4:
Sylvia: Ohhh! I bet your sister is real elegant an' beautiful an' all. Nothin' like me.
Claude: That's not true! I find you very attractive, and you have a grace all of your own.
Claude: Of course. I'd never tell a lie.
Sylvia: Wow! No one's ever said anythin' so nice to me! Er.. I feel funny inside... You are... so kind!
Sylvia's lover convo with Levin is quite heartwarming as well, questionable patch translation nonwithstanding. And then there's Levin's talk with Leen in chapter 10...
Arden's lover convos with Ayra and Fury are ridiculously sweet.
Also Lex and Tiltyu's convo. "Look, we've both been dealt a crappy hand. I wish we could've been together longer. I will cherish every single moment we had."
Adean's convo with Azel in chapter 4 can bring a person to tears of joy when you consider this is not only Azel's dream come true, but that she tells him just how happy she is to be with him.
Her convo with Midayle is just as sweet, for the same reason plus the element of devoted Bodyguard Crush.
Alvis telling Sigurd how much Azel means to him in chapter 1 of the game is heartwarming enough, but the Oosawa manga takes it Up to Eleven. During the wrap-up of the Verdane arc, Alvis actually talks to Azel in person and tells him he loves him.
Alvis: If by chance, some time in the future...no matter what happens, I always want you to believe in this fact.
Levin telling Fury he loves her in chapter 4.
Fury: Ah, so you and her were... I'm sorry. I didn't know.
Levin: Fury! You've got it all wrong. When I was a little kid I thought your sister was hot. But that was then. Now it's you.
Levin: I love you, Fury...
In the Oosawa manga, Levin is knocked out cold by a Sleep Staff and Sylvia risks her life to rush to his aid, telling the Bishop how wonderful he is as she holds him in her arms. Sylvia's feelings for Levin in general double as this and Tear Jerker material; the manga takes game!Sylvia's huge crush on him and adds a heartbreaking reasonwhyshe clings to him so. Makes it all the sadder that she doesn't end up with him in this manga.
And as a call-back, in chapter 34 of the manga she and Fury interact again after Sylvia's Tear Jerker of an explanation of her and Levin's bond... and not only they get along much better than the last time, but they smile to each other and promise to be friends. A very sweet and refreshing subversion of the usual catfights over a guy in the middle of a Love Triangle.
Azel's talk with Talito in chapter 4 of the game displays their bond of childhood friendship beautifully, and strengthens their Relationship Values at the same time.