The fact that this game exists. How? In The Legend of Zelda: The Wind Waker, the king wished on The Triforce for Link and Zelda to have hope for the future and to find a new land for themselves. By Spirit Tracks, they managed to achieve all that.
The title screen features ghost-form Zelda, gleefully hovering around Link's Cool Train, giggling, smiling and enjoying herself and her newfound freedom like never before. AWWWWWWWWWWWWWWW!!!
A small moment, but every time Link gets in his train he salutes. Even if there's nobody there to see him, he's an engineer. The practice of "service with a smile" has clearly been instilled in him, and he's going to salute whether or not there's anyone around.
Hey, Zelda's always around him, though that makes it even better!
Spirit Tracks has these in droves. After defeating Byrne, Zelda gives a speech on The Power of Friendship, after which she and Link stare romantically into each other's eyes...which is somewhat diminished by the fact that Zelda is stuck inside a huge and scary suit of armor.
There's also their adorable little victory high-fives.
This whole scene quickly turns to funny as they break out of the Moment to find that Byrne is leaving.
After regaining her body, Zelda gives Link a big hug. Link, for his part, seems a bit flustered.
And of course, the big one comes just before the credits, as Link and Zelda hold hands as they gaze into the sunset.
The "Engineer" ending scene after the credits. Zelda is signing some royal papers, and Link sounds his train whistle as he travels past the castle causing Zelda to get out of her seat and wave at him joyfully out the window. The End. *Cue train whistle in the distance*
The "Warrior" ending throws in a bit of humor. While signing royal papers, Zelda hears and checks on Link sword-fighting outside. She happily greets him... and Link, apparently distracted, gets waylaid. He's alright though, and Zelda waves at him.