Clothes Make the Legend: By this point, Link's iconic attire has become the standard uniform for the royal guard (probably in honor of the Link that founded their homeland; the same one from The Wind Waker). This Link ends up wearing it because he has to sneak out of the castle and dresses up as a royal guard to do it.
Cool Train: Both in and out of universe. Better yet, you can upgrade it to many other looks, all cool.
The Dulcinea Effect: Despite having just met Zelda, he's willing to throw himself between her and the guy who just kicked an adult master swordsman's ass.
Identical Stranger/Identical Grandson: No connection is ever made between this Link and Wind Waker/Phantom Hourglass Link, but whatever the case may be, he is identical in almost every way. The character model and animations are reused from Phantom Hourglass.
Instant Expert: He's a train engineer, not a warrior, who needs to be trained how to use a sword at all. He's instantly an expert at every weapon and tool he picks up from that point onward.
Parental Abandonment: Who and where his parents are is completely unknown, despite his apparent young age.
Precision-Guided Boomerang: Even more precise than normal for this trope, since you can draw the path the boomerang will take with the stylus and, barring it smacking into anything solid, it will follow it exactly.
Wall of Weapons/Hammerspace: By the end of the game, he's carrying a sword, shield, pinwheel, boomerang, whip, bow, and probably the optional bombs. And that's not counting the pan pipes, stacks of letters, potions, and treasure.
Distressed Damsel: Strangely, both played straight and played with. Her body is kidnapped and needs to be rescued for most of the game, but her spirit accompanies you and grows into her Badass Damsel role over time.
Expy: When possessing a Phantom, her appearance and demeanor are really close to Alphonse Elric.
Identical Granddaughter: She looks exactly like Tetra did when she turned back into Zelda in Wind Waker. She's also identical to her ancestor from The Minish Cap — someone who, according to Hyrule Historia, lived well over a hundred years before even The Wind Waker.
Ironic Echo: After Cole betrayed Byrne, Zelda stated that when she gets her body back, she's "gonna have a couple of words" with Byrne (which her motions imply that she wants to beat him up). Byrne later reminds her of that statement when holding Malladus back so Zelda could regain control of her body (and ultimately paying the price for it).
Legacy Character: Somewhat unique amongst other Zeldas in that she is confirmed to be directly related to another. Specifically, according to Word of God, she's Tetra's great-great granddaughter.
Properly Paranoid: She wanted to have Link aid her in escaping the castle, as she suspected that Chancellor Cole was not trustworthy. She's right. Unfortunately, Cole doesn't allow her to live long enough to reveal his plans to anyone else.
Red Eyes, Take Warning: While possessing a Phantom, her glowing eyes will change from pink to red when she is angry.
Royals Who Actually Do Something: On top of aiding Link in his quest, she is the only Zelda in the entire series that's shown actually handling the political aspects of running a country (or at the very least, dealing with paperwork).
The main villain of Spirit Tracks is an evil demon that was sealed in the earth long ago, bound by the Tower of Spirits and the Spirit Tracks themselves. He makes his return when Chancellor Cole steals Zelda's body and intends to use it as a vessel for his spirit.
Large Ham: While having three lines total in the whole game, none of which have voice acting behind them outside of the trademark Zelda "Hyyaaaahhh!", each of them still manages to be incredibly hammy.
Smug Snake: Subverted. He is incredibly annoying and perpetually smug, but is actually an effective threat.
The Unfought: He only aids in the first round of the final battle, he is never fought himself.
Byrne (or Staven in the European English translation) is Chancellor Cole's right-hand man in Spirit Tracks. He is a renegade member of the Lokomo tribe who turned away from the Spirits of Good and served the Demon King. After Cole betrays him, Byrne helps Link and Zelda defeat Malladus.
Arm Cannon: His main weapon is his oversized mechanical arm that he uses as a grappling hook.
A woman of the Lokomo tribe, who is in charge of protecting the Tower of Spirits. She has powers similar to a Sage's, and is often referred to as one by Zelda (along with the other Lokomo Guardians), but she doesn't seem to agree with this term. Anjean apparently used to be Tetra's (The Princess Zelda of The Wind Waker) best girlfriend after they met in New Hyrule, which explains them wearing their hair in a similar fashion.
Ascend to a Higher Plane of Existence: Her ultimate fate, along with Byrne and the rest of the Lokomo, who depart to the heavens after Malladus' final defeat, confident that New Hyrule is safe in Link and Zelda's hands.
Cool Old Lady: She seems to have picked up one or two habits from Tetra, which makes her an interesting character, especially standing next to Zelda, who is descended from Tetra but a little different in personality.
Magic Music: The Spirit Flute used to belong to her, until she gave it to Tetra.
The Obi-Wan: Link's older mentor who gets sidelined by injury early in the game.
Retired Badass: Although it's more of an Informed Ability, since the one and only time we see him with a sword he gets his ass handed to him. Granted, the person doing the asskicking is insanely powerful, but it still undermines the "badass" part.