Basically any sisterly scene between Luca and Cloche, both before and after they learn that Cloche is Leyka. One standout moment among those is Luca and Cloche wanting to retrieve a memento of Reisha from her grave and Cloche, who had celebrated her birthday on what was really Luca's, finding out that her true birthday was that day courtesy of Luca secretly finding out from Reisha before she died and preparing a gift for her. It comes full circle when Cloche again gives Luca her original birthday gift from back in Phase 1 that Luca destroyed in a fit of rage, but Cloche still held on to.
As well as any scene between Cocona and Croix.
In Jacqli's ending, Croix confesses his feelings with song, which later turns into a duet with Jacqli. Note that this is the only song (in the games themselves) with a male singer which makes this event even more significant.
Reisha's lullaby and what it stands for.
The lyrics themselves describe the bond between the Maiden of Homura/Fuero and the Maiden of Mio/Aqua.
Luca's late birth-mother Arshe taught the song to Reisha, her close attendant. It ends up passed on to both of the Maidens from both of their mothers.
It calls back to the happier times of the Trulywaath family. Kinda makes you turn on the waterways when you see their early childhood memories in the final level of the Infelsphere or when Cloche regains those memories in her Cosmosphere...
Amarie and Leglius reconciling after the battle between the Sacred Army and the Grand Bell has ended. It's shown that behind Leglius' dutiful personality, he had a soft spot for Amarie and cares about her despite being a Sacred Army spy. He also admits that she reminds him of his deceased daughter. Amarie's also endearing enough to make the battleworn knight actually smile, something that's rarely seen in the game.
Combined with Tear Jerker, Reisha's second and final song Eternally Bonded. It has no effects (Reisha is human, thus it's not true Hymmnos), but like the above example with Croix, it's sung overflowing with feelings of love, sadness, and happiness, in hopes that that her daughters would understand it, and in Luca's case, forgive her for her neglect.
Try to listen to the song's two final lines and read its translation without crying... Oh, life that was given birth in a shining day, your gentle smile will never disappear, and it will bloom eternally...
With the mechanics of Hymmnos in play, the fact that two humans, Reisha and Croix, use Hymmnos to convey their feelings the way Reyvateils do. In a technical sense it shouldn't be effective, but the effort they put into learning the language and utilizing it for others is what makes it powerful and touching.
It's not apparent on a first playthrough, but Frelia asking Shun if he's Enja becomes one in hindsight. Despite Shun no longer having a human form and the two not seeing each other for hundreds of years, Frelia never forgot him. And how did she recognize him even in a new body? She recognized his personal tics of how he would look beyond her rather than at her when talking to her.
Watching the party members explore the new continent of Metafalica during the end credits and being able to witness them enjoying the miracle they created. What's especially adorable is Cocona using Shun as a pillow when she decides to rest up.
Infel giving last-minute encouragement to Cloche when she starts to slip up singing the song to create Metafalica. Deep down, while Infel may have had her ulterior motives and used her, she still cared about Cloche's well-being enough to put her trust on her despite her doubt that she could succeed.
Croix learning Jacqli's true name, Mir. While more willing to open up to the group, Mir still couldn't completely open up because of her personal dilemmas in the past. Willing to tell Croix her real name is a sign that she truly trusts him to know who she really is and, what's even better, is that Croix begins to refer her by her real name afterwards in her route.
