* AccidentalInnuendo: "Hey, Link! Tap me! Tap meeeeeee!"
* AnticlimaxBoss: The second phase of the final boss almost never attacks you and does piddling damage when he does. It doesn't help that the Chancellor Cole fight immediately before was both harder and '''much''' scarier.
* AwesomeMusic
** [[https://youtu.be/g1KtpD018WY Stagnox's theme.]] It helps that it gets a remix in [[https://youtu.be/XExZ3U1jI_Q Skeldritch's theme.]]
** [[https://youtu.be/2l4fjQBMckE Cragma's theme,]] which is a very good remix of [[https://youtu.be/B0sves087iU Fraaz's theme.]]
* BreatherBoss: Phytops, the third boss, especially compared to the bosses before it. It only has two attack types, an easy-to-avoid projectile attack and a whipping attack that only takes off half a heart, and it's nowhere near as involved to beat as Stagnox and Fraaz.
* BrokenBase: The train. What's interesting about it is that fans tend to like it or dislike it depending on their view of how the franchise should be:
** People who like Zelda games for their puzzle solving, combat and story tend to be OK with it. They consider it brings some fresh air to the series, especially regarding atmosphere, and that it fits in a handheld game.
** People who like Zelda games for their sense of exploration and discovery are the ones who tend to hate it, since they think it utterly kills both characteristics without leaving a trace while adding the stress of constantly trying to avoid the Dark Trains takes all the fun out of the world map.
* BestBossEver:
** Fraaz is a Keese-like creature that can use both fire and "icy fire" to attack, and has probably one of the catchiest boss themes from the game (sharing parts of it with Cragma's theme). Pair in that it uses the boomerang much better than the fight against Blaaz in ''Phantom Hourglass'' and that the boss is a considerable step up in difficulty from Stagnox and it definitely earns a place.
** Cragma is a giant stone golem residing in a pit of lava, who foolishly grants you access to a mine cart that you ride up and around the chamber, filling his [[AttackItsWeakPoint glowing weak points]] with arrows.
** Byrne, TheDragon, against whom Phantom!Zelda assists, and she's capable of yanking him right off the pillars he's balancing on. In the fight's second phase, she can grab and wrestle with him when he does a darkness-powered dash attack, allowing Link to strike.
** Skeldritch, a skeletal totem pole of sorts, in which you can ''catapult'' the boulders it throws right back at it.
** [[spoiler:The Demon Train. Train vs. train fight. Unlike the Ghost Ship battle in ''Phantom Hourglass'', it's not ridiculously cheap, and there are simple and intuitive counters to each of its attacks. Plus, its final weak point is its enormous face, and it's oddly satisfying to pound it full of cannonballs and see it writhe in agony.]]
** Malladus itself. [[spoiler:Especially the final phase, where he turns into an enormous demonic blue warpig-like creature, with horns and red hair. Sound familiar? And that's not even getting into how Link and Zelda -- back in her body -- team up to fight the very Ganon-like creature, ''and you have control over both of them''. It bears repeating: ''Link and Zelda team up, both under the player's full control, to fight a Ganon-like final boss.'']] And then the music complementing the fight. A remix of the overworld/title theme, with all of the Lokomo's instruments playing a part in the song, that's a perfect continuation of the duet you played with Zelda moments before. The icing of the cake is the absolutely glorious [=CMOA=] that ends the battle: [[spoiler:Link and Zelda wielding together the Lokomo's Sword ''and thrusting it into Malladus forehead in a SmashingSurvival event''!]]
* CatharsisFactor: The Dark Realm, where you get to pick up Tears of Light, make your train invincible, and run down the bastard Armored Trains that you had to dodge the entire game.
* CounterpartComparison:
** Fraaz is often compared to both [[VideoGame/TheLegendOfZeldaOcarinaOfTime Twinrova]] and [[VideoGame/TheLegendofZeldaPhantomHourglass Blaaz]], due to how it's fought as well as its theme in general.
** Skeldritch is easily comparable to Stallord, including how the player needs to [[MakesSenseinContext break Skeldritch's spine]] to expose its weak spot and the player needing to attack its head in order to completely kill it.
** [[spoiler: The Malladus-possessed Cole]] is often compared to Ganon. They look very similar in design, arrows of light are required to beat him, and how Link and [[spoiler: Zelda]] perform the killing blow is almost the exact same as Ganon's in Ocarina of Time.
* DemonicSpiders:
** Dark Trains. They're invincible, and hunt you mercilessly on the tracks. Heaven help you if you're sandwiched between two of them on the rails. Why? Because they kill you in a single touch! You can slow them down temporarily with five cannon strikes (useful if you're reduced to reverse-running from one), but if you attempt to do so, watch out for the ''other'' one circling behind you. Then there's the armored versions of them. Same one-hit-kill if you run into them, but they'll ''actively'' pursue you, going so far as to turn around on the track to continue chasing you should you manage to fake them out, and unlike their unarmored cousins, can only be slowed down ''very'' slightly with each hit. [[spoiler:You finally get to kill those bastards in TheVeryDefinitelyFinalDungeon. And it's so sweet to see [[DeathByIrony them destroyed by you running through them]].]]
** The Rocktites combine TheJuggernaut and AdvancingWallOfDoom into a single package of player frustration.
* EarWorm:
** [[http://www.youtube.com/watch?v=5W_bFLwB0WY The Overworld theme]] a.k.a the theme that usually plays while riding on the train.
** [[http://www.youtube.com/watch?v=_CpyO0wrAQs In The Fields]] (the on-foot outdoors theme) will be stuck in your head within just a couple times of hearing it.
%%* EnsembleDarkhorse: Byrne.
* FakeUltimateMook: Cragma. He's absolutely everywhere in advertising materials, but the fight against him is extremely underwhelming (shooting him in his weak points, [[EyeScream then shooting him in the eye]], then slashing his head, with little variation between forms).
* GoddamnedBats: Most of the enemies you encounter while driving your train, but especially the big spiders (take two hits to kill, and wobble erratically after the first hit), cave bugs (appear in large groups and circle the cave rapidly before diving on you) and the tiny flying elephants that are often difficult to see, let alone shoot. The ranged attackers can become a problem if you're distracted by something else or can't turn to face them quickly enough. All enemies do 1/4th of your train HP per hit, making death by monster-spam a serious danger.
* HolyShitQuotient: The FinalBattle, one of the most epic in the entire franchise, filled with moments that almost sent a lot of fans into a joy seizure.
* MemeticMutation:
** While at first, several topics used the pre-existing "This topic sucks and is now about trains" meme to discuss the game, it soon became known as "''Soul Train''" over several boards.
** Ever since the last trailer, the meme "The Phantom wears a dress" surfaced.
** The Demon Train was also known at one point as the "Ganon-train" due to how similar it looked to cel-shaded Ganon. Of course, Ganon never appears in this game, but the name has still stuck.
** [[http://knowyourmeme.com/memes/choo-choo-motherfucker "Choo Choo Motherfucker"]] originated on a Website/FourChan post about the leaked concept art of Link in a conductor's outfit.
* {{Moe}}:
** PlayedForLaughs whenever Zelda possesses a Phantom. For the rest of the dungeon, you're followed around by half a ton of loudly clanking armor that [[EekAMouse recoils at mice]], acknowledges your orders with adorable squeaking noises, and makes girly poses whenever you talk to her. Even the other Phantoms notice that she's "CUTER THAN USUAL".
--> '''Random Phantom Guardian''' (to Zelda): SOMETHING'S DIFFERENT ABOUT YOU TODAY.
** Zelda's dialogue when you leave the Dark Ore Mine plays it straight.
--> '''Zelda''': Choo-Choo!
* NightmareRetardant: While most players agree that Malladus in Zelda's body looks creepy as hell, his look outside of possession is more likely to make you laugh than scared, with those goofy-looking teeth.
* ScrappyMechanic:
** The Lokomo songs can be annoyingly touchy, both in requirements and in controls (the mic seems to make a lot of double notes from a single blow, and it's a real pain in the ass to hit two notes not next to each other without hitting any of the ones in between). And relying on the microphone makes them simply impossible in places with a lot ambient noise, such as on a train or airplane, or in a public setting... in other words, places you would want to use a portable system. It also gets a lot harder simply by not being a musical person. There have been tales about people trying over a dozen times before handing the game to their more musically-skilled friend who cleared it in two tries. Success in a non-music game's main quest should not be tied to the player's musical skills.
** Some people have noted that Phantom Zelda's AI has certain weaknesses that can make controlling her and Link in tandem a rather annoying task, especially in midboss and boss fights.
** Some find the warp gates to be complicated and annoying to use and implement. If you're lucky and can figure out proper, distinguishing symbols to mark them by, it may work out, but otherwise...
* SpiritualLicensee: [[http://tinyurl.com/lb43zo5 There]] [[http://tinyurl.com/oaae94f have]] [[http://tinyurl.com/lspzmoc been]] [[http://tinyurl.com/lf8yng2 comparisons between]] this and ''Manga/FullmetalAlchemist''.
* ThatOneBoss:
** Fraaz. He's surprisingly hard for being only the second boss in the game, and he's the savviest enemy in the game to boot; his main form will aim where the game "thinks" you'll be when his shots reach you - he's the only non-overworld boss in this game to do this accurately - and [[spoiler: after the first form cycle, he'll destroy the torches you were using against him]]. (Phytops will also try to "lead its target" with its goo shots in some parts of its fight but, unlike Fraaz, if you keep moving in the same direction Phytops will usually miss.)
** The three-part final boss requires some crazy nimble reflexes with your stylus, likely enough to induce arthritis. [[spoiler:This applies to the Chancellor Cole fight, guiding Zelda up to Malladus while destroying Cole's [[WhyDidItHaveToBeSnakes magic mice]], and [[TennisBoss batting away Malladus' fireballs]] while Zelda charges her magic. Thankfully, the final scrap with Malladus proper is easier.]]
* ThatOneLevel:
** [[spoiler:Destroying the Armored Trains in the Dark Realm.]]
** The final floors of the Tower of Spirits are the most devious part in the game, since they're packed with a vast array of puzzles, hazards and passageways that can only be tackled by out-of-the-box methods that make use of ''all'' of the items in the inventory and clever cooperation with the various types of Phantoms Zelda can possess. At one point, Link and Zelda also have to find ''three'' keys to access three different rooms whose puzzles can only be solved when all of those rooms are available for access. Near the end, there's also an invasion of several powerful enemies (including three high-tier Geozards) where Link must triumph while avoiding a pitfall.
* ThatOnePuzzle: The door to open the Ocean Sanctuary. Different in that it's not actually difficult to figure out, but the door won't accept the symbol you draw unless it's absolutely perfect.
* ThatOneSidequest: The Dark Ore sidequest. You have to carry some ore that melts in sunlight halfway across the world map, and the only way to keep your cargo intact long enough is to go through a tunnel - inhabited by a [[GiantEnemyCrab Rocktite]]. Made tougher by the fact that you're also harassed by smaller ones. And getting hit causes you to lose some precious ore, so the bottom line is that you have to fight one of the tougher bosses in the game ''and'' take no more than one hit. There is a bit of a GuideDangIt cheat, though... The boss appears as soon as you enter it after unlocking the track, but only in the direction you need to take with the ore. You can beat it, then go pick up some ore and deliver it at your leisure, since the Rocktite won't ever respawn until you save and quit (the smaller enemies do, but they aren't as bothersome without the big one to focus on).
* TheyWastedAPerfectlyGoodCharacter: Many of the bosses could have interesting lore behind them, Fraaz and [[spoiler: Skeldritch]] being some of the first that come to mind, but unlike other Zelda games Spirit Tracks never gives any hints about the bosses.
* ToyShip: Even some fans who are diametrically opposed to {{shipping}} Link/Zelda will acknowledge the adorability of their bond in this game.
* UncannyValley: The [[http://vignette2.wikia.nocookie.net/zelda/images/3/3a/Demon_Train.png/revision/latest?cb=20091111023844 Demon Train]]'s face falls into this category.
* UnderusedGameMechanic: The Battle and Tag modes from Phantom Hourglass return, and are even one of the most advertised features of the game. However, unlike Phantom Hourglass, Spirit Tracks doesn't have the ability to connect to other players over the internet even as an option. Which is unusual, since Phantom Hourglass before it DID have wi-fi capabilities and Wii Connect 24 (Nintendo's wi-fi service at the time) hadn't been deactivated for another 4 years.