Finally finished this game so finally able to read this thread. A good set of choices, although mine are notably different.
1. Garnet running to Zidane. Now, I found the ending quite a bit... long. And I totally knew what was going to happen without having to think about it (and this part wasn't spoiled for me, thankfully). But the running bit just made the moment, and the punching of the chest just added to it. It felt real, and that's a rare thing in gaming these days. Touching. I'm not normally a guy for the mush and in this game I wasn't massively drawn in by their relationship, but in this particular case I was suckered in completely.
2. Odin vs. Cleyra. This hit harder than the Alexandria destruction for me because it was complete and utter destruction of an entire city and the city was gone. Not just rubble. It was GONE. Forever. And that hit hard. That really showed off the power of the Eidolons. I felt far sadder than I did against Lindblum or, later, Alexandria because of how it all went down. I'll skip the Lindblum/Alexandria stuff for being similar to this one.
3. Quina and Vivi get hitched. D'awwwwww. I so happy.
4. Zidane's origins. I'm so glad this part didn't get spoiled for me because for some reason it never occurred to me that he might be from another world, mostly due to there being other kinds of talking animals around. It just seemed normal, in a way. But seeing another like him the moment you get to 'the other side' was a surprise and I loved it. To be honest I didn't care much for the drone-ness of them or the purpose of Zidane or whatever, I just love that I didn't expect him to be an ALIEN.
5. Black Mage Village in general. Just gorgeously innocent. I love it. My favourite part is just before the end, when everyone is learning about each other. The 'stopping' talk fits in here, too.