Anticlimax Boss: Cleon, surprisingly enough. The story makes him up to be quite the foe, and he could have been if he'd been fought with a one or two man party like many other bosses, but instead he had the misfortune of fighting Valkyrie who flatly ignores his signature ability. If you even have to heal once during this battle it's because the mooks beforehand left you injured. (Of course he gets another go at it soon after).
Also Cari, especially given what comes immediately before and after, but that was a given considering her powerset and role in the story.
His attacks are pretty devastating, but the final boss battle with Ketsu is much shorter than the battle immediately before against Ariel, and you get a full heal and an Eleventh Hour Superpower buff partway in.
Most of the battle themes, particularly "No Education", "A Toccata Into Blood Soaked Darkness", and "Shroud vs. Sparrow".
Considering that a lot of the soundtrack comes from Crowning Music factories like Apocalypticanote See above re:"Shroud vs. Sparrow", also known as "Path", Nightwish, and Sonata Arctica, this isn't entirely surprising.
Goddamned Bats: You will learn to hate the bats that creep around in the Gallian Church in the first arc of the game.
Demonic Spiders: During the last chapter Valkyrie has to fight several huge groups of mooks. Genre Savvy would suggest that her new powers would make this a Curb-Stomp Battle, and indeed they're barely capable of scratching her with any of their attacks, but every one of them can choose to heal almost as much damage as she can dish out in one turn at any time they feel like it, either for individuals or the whole group. Or throw up a shield that greatly reduces how much damage she can do, exacerbating the healing problem. And the group healing spell also cures all status effects.
Several in later arcs. Andau's death, Rana's betrayal and Laurel getting her wings are powerful moments, but the most moving scene in the game is arguably The Rain of Fire scene, where all the races on Solest put aside centuries of conflict to help each other in the wake of the disaster. All the more sad because it doesn't last.
When Gino died! This troper was holding back tears.
Gabriella's exile from her academy after Andau turns her. She may been a bigotedbitch while human, but seeing everyone she knew and loved completely turn on her actually makes you feel sorry for her.