The director's cut of Tales of Destiny has so many, especially in Leon's mode. Some examples include his shopping trip with Marian between parts 1 and 2. Everything in the scene is full of win starting from Leon straightening out his clothes as he waits for Marian and in the end where Marian acknowledges him as adult. Other heartwarming moments occur during Leon's bouts of motion sickness. In one instance, Chaltier tells Leon that its okay for him to start thinking of other people as friends, later he and Stahn have a chat about "guy stuff", and in another, Rutee comforts him and they have a nice heart to heart. Also, after the events in Aquaveil, Chaltier declares that Leon is the only master for him (after briefly being loaned to Johnny).
In Stahn's side, on the way to Moreau, he and Rutee get trapped in a cave and get to know each other as they wait for Leon's group to get them out.
From the original game there's the scene on the Draconis between Stahn and Rutee and their farewell scene at the end of Part 1. Especially adorable is how in the latter Woodrow, Phillia and Leon make up some excuse to leave them alone.