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!!!
And then Link invites her to stand in the cab with him. The whole scene is incredibly sweet.
Niko being the narrator of the opening credits. He was a minor character in Wind Waker and the narrator of the opening credits of Phantom Hourglass so seeing him again a hundred years later telling the story of how his crew helped to found New Hyrule can make a few fans of the previous two games be filled with nostalgia.
Him being Link's roommate and having an Intergenerational Friendship with him makes this all the sweeter because Link reminds him of a certain crew mate of his, obviously implied to be the Link from Wind Waker and Phantom Hourglass. It appears some friendships do transcend lifespans.
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!
Linebeck III existing pretty much shows that Linebeck had a successful life. Considering the adventures the player and the previous Link endured to defeat Bellum, it feels rewarding that the Ensemble Darkhorse made it big in the new land his friend discovered.
Anjean proves to be this by revealing that she used to be Tetra's best friend when she and her Link discovered New Hyrule. Not only did she and Tetra hit it off well, but she still values her friendship with her so much that she decides to help Zelda and Link without hesitation.
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.
When you first arrive at Papuchia Village, Zelda asks Link to go swimming with her once she gets her body back. If Link says he can't swim, Zelda offers to teach him.