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!!!
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.
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!
The fact that this game exists. How? In The Legend of Zelda: The Wind Waker, the king wished on The Triforce that while he couldn't save Hyrule itself, he wished that the remaining descendants to have hope for the future and to have a new land for themselves. By Spirit Tracks, they managed to achieve all that.