Everything from Vyse giving Ramirez a traditional air pirate send-off, the scenes depicting life returning to normal throughout Arcadia, to the music that plays during the end credits, and final scene of the newly christened Albatross II sailing of toward the horizon. It all feels like a fitting end to a memorable journey.
The Moonfish/Piccolo/Moon Hamachou Sidequest, where you find moonfish around the world for the strange pet bird of Maria. For even a long-term fetch quest, there's a lot of benefits for doing it (the rare item rewards, learning of the backstory behind the Doctor, Ramirez, and Maria's family, continuing Piastol's sidequest, and obtaining one of the final discoveries), but most importantly, you're helping a traumatized orphan out of depression, and her interactions with Vyse and Piccolo (her pet) are adorable. After this sidequest, you can fight Piastol for the fourth and final time. Vyse then tells her that her little sister Maria is alive and that she should see her. Their reunion tops off these sidequests perfectly.