The two-parter in Natural where Akari has to say goodbye to her gondola. It hadn't been treated as a character, but as you see the history behind it and come to realize how important it really was, the dream sequence where the gondola's spirit, as an old man, asks Akari "Could you row me for just a little longer?" In the next episode, when the spirit places an umbrella over a sleeping Akari, while the lyrics "Safe on a rainy day/ I'll miss you..." play, it's just so beautiful and sad at the same time.
Alice's promotion in Origination. First we see her throughout the whole episode showing how she'd grown since she was that shy, quiet girl way back in Animation. Then, she shows how great an Undine she is as she takes Athena for a tour. In the lock, Athena tells her not to worry about her singing, and just to sing. Then, on Hope Hill, where all her friends have gathered, she sings a beautiful song. Seeing Athena take off Alice's first glove gives a sense of fulfillment to the episode. Then, she took Alice's other hand, and Athena gives a short speech about how important young Undines are. With that, she takes off the other glove, and dubs Alice "Orange Princess." The clincher comes when Alice bursts into tears and thanks her friends for everything they've done The promotion is so incredibly well-done.
Athena reached to remove the other glove as the discussion about singing and the actual song request were the biggest elements of foreshadowing that Alice was secretly being given both promotion tests at the same time. It's made even more powerful after having spent the entire series up to this point wondering, "Why hasn't Alice been promoted to a Single yet?" She had to finish middle school first, but the fact that she gained the skills to go straight to Prima before graduating testify of her ability.
The last episode. Dear god, the whole episode. Every part of the whole episode. The mailman... the ceremony... the flashback scenes and the hug... and Ai too. All of it. Just... wonderful. All the wonderful things on Aqua that you've seen in the past 52 episodes just flow through you like Neo-Venezia's canals, spreading love. And you just can't help but cry...
Episode 12 of the first season made. Just...the scene where the water is released.
The episode where Akari delivers the old letter to the grave of the recipient, knowing the message was recorded by his wife who had yet to hear of his death.
The farewell ceremony for the nightshine chimes, especially when one realizes that Akari treated it as more than a tradition.
Let's face it: Every single episode has at least one, especially when watching the series for the 2nd+ time. The clincher? Most of them are because of positive events.
From the manga, there's Akari's final meeting and farewell with Cait Sith.