Just thought of a good one. That bit in the lead-up to stormblood...
when they have to drag Yda/Lyse away kicking and screaming so Papylamo can try to seal Shinryu. If i remember right, i refused to leave the first time i watched and he used fluid aura(or something similar) to knock me back onto the airship.
Theres a stone-cold callback to Haurchefaunt in the DRK questline(one of the Myste bits from SB).
The shade born of Gallien's memories tells you of how he always wanted to meet you, a larger-than-life hero...unaware that he eventually did at Little Ala Mhigo. He laments his fate, wishing he could go back and convince his former self not to place his trust in the Griffin...but if such things were possible, you wouldn't have a broken shield, now would you?