Warning: Spoilers Off applies to this page. Proceed at your own risk.
In the North American Wii U version, the fairy who warns Impa and Sheik is identified as Navi. Though all other versions simply identify the fairy without an actual name.
Whilst preparing to obtain the Master Sword, Impa wonders whether Link is truly ready for such a task. The response?
Zelda: Because I believe in him.
Lana: I believe in him, too!
What makes it even better is how Lana stutters and stammers through her response. Not because she's lying, but because of the way she's trying to actively support Link without making it obvious she's fallen for him.
Any time the group pull a Big Damn Heroes, which also counts as a Crowning Moment of Awesome.
The first example would be when in the Temple of Souls, Link is outnumbered by Dark Links and is about to be taken down, when Lana comes to the rescue. Unfortunately, even her power isn't strong enough to fend them off, but luckily Midna, Fi, Darunia and Impa come to save the day.
Next, while in Gerudo Desert, Lana is the one who is outnumbered by multiple enemies. Using her spell book, she opens up three portals and summons back Fi, Agitha, Midna, Darunia and Ruto. No sooner after entering the battlefield, they crowd round Lana protectively, prompting a happy and content smile from Lana.
What really makes this nice is that there's no indication she's even given them any warning about what's going on. For all we know, Instant Runes showed up, they recognized Lana's magic, and they decided to lend a hand.
Lana attempting to comfort a dying Cia after the latter's defeat at the hands of Link.
Ruto sitting on Darunia's bicep as they wave goodbye one last time to Link, Lana and Zelda is rather cute.
In the final level, when Ganondorf appears, each of your allies will do everything they can to stall him while you try to capture his base and reduce his power, knowing fully well they don't stand a chance against him. You'll really want to accomplish this as quickly as possible to protect your allies.
Or you can invoke this yourself by shielding your allies from his wrath and taking him down yourself, ultimate dark power be damned.
Midna's fighting style is a minor one. She tamed, possibly even created, packs of twilight wolves to fight for her just like Wolf Link does, which can easily be taken to mean she misses her era's version of him enough to want something that reminds her of him. The fact even her Twili form has them can be taken to mean she tamed/made them during a time of peace to be her pets.
Fi has some moments where she proves she's Not So Stoic. Her Item Get! pose shows her actually smiling, she participates in two Big Damn Heroes moments, and in the penultimate level, even though she says the group has very low chances of winning, she says she doesn't care and resolves to fight anyway, followed by wondering if this is what trust is.
Link's victory scene if his weapon set is Epona. It's a greatly touching demonstration of the friendship and trust between our hero and his faithful steed.
The interactions between Link and Zelda as the story progresses. It's subtle, touching, and sweet to see how much they come to trust each other. And it's further proof that, no matter the era or the situation, those two will always gravitate towards each other. Easy to see why Cia got jealous, in that regard.
Lana never giving up on Cia, ever. Even teaming up with her in Cia's final Legend Mode level after all of Cia's allies had either betrayed or abandoned her by that point, knowing Ganondorf was going to win anyway.
A minor one, but Young Link's strong attack button: usually, he pulls out his ocarina and plays it to turn his SP gauge into Magic. But what happens if you do it when the magic gauge is already full? He puts on the Keaton mask and lets out a roar before putting it away and giggling. It has no real use, but it shows that, despite all the battles he has seen, he's still a child at heart.
Another minor one- Ganondorf's chapters involve him, Girahim, and Zant working together. This just seems heartwarming for some reason. It gets better if you play as another villain in Free Mode.
Similar to the one above, the Dinolfos and Lizalfos Chieftains are incredibly loyal to Volga, continuing to follow him even after he's brainwashed into doing Cia's bidding. They do everything they can to protect him from her in the first part of Cia's Tale in Legend Mode, and in the last part, apologize to him in clear pain for failing him. Their loyalty to him is almost jarring after seeing how badly Cia herself utterly fails to keep anybody's loyalty and must brainwash her minions into following her in the first place.
Hyrule Warriors Legends gives Cia and Lana a happy ending with the new Wind Waker campaign in Legend Mode, with Lana, Link, Tetra, and King Daphnes working together to rescue Cia and her magic from the clutches of Phantom Ganon. Cia pulls a HeelFace Turn and the campaign ends with Cia and Lana going back to their job of guarding the Triforce, but this time, they go together.
Have Link go to protect the Commander during the Temple of Souls mission. Cia is shocked Link would bother to do anything for her after everything she did. Link, via Proxi, says that nobody blames her for what Gannondorf made her do, and now she needs protecting, so he's going to protect her. Cia's response is the sincerely thank him, without a trace of obsession in her words.
Cia: Link?! You'll help protect me too?
Proxi: You're not the enemy anymore. And you need protection.
Cia Heh....always the hero...
Especially heartwarming since it's very clearly Link's words. Possibly the only time he's ever really been the one to talk.
Despite what you might think, Lana's goals get second-guessed by absolutely nobody. Everyone knows what Ganondorf is capable of and if Lana's willing to vouch that the real Cia is worth saving, that's good enough for them. In the final cutscene, Zelda and even Impa aren't the slightest bit suspicious, nor do they hesitate to let Cia keep the Triforce of Power.
A minor one in Linkle's story: how easily Midna was willing to break the crystal and return to her cursed form to save Zelda.
The conclusion to her storyline as well. After ditzily stumbling through the wrong place at the right time, she finally gets to save Hyrule. The captains storming the field in the final leg of the battle, cheering her on and returning the favor for being saved in the field, is a nice touch.
To borrow from a quote from Sherlock: Link saved Hyrule. Linkle saved lives.
And during the final cutscene, despite knowing it's not true Impa humors Linkle's declarations about being the Legendary Hero. The implication is that even the difficult-to-impress Impa found Linkle impressive enough that she's entitled to a (very cutesy) Badass Boast.
Linkle is a Cucco wrangler by trade and several side missions in her levels involve helping various Cuccos out. How do they respond? By acting as her entire army! They love her that much!
One for Toon Link. Like with the other Links in the game, he can't talk, so someone has to talk for him. But it's not a fairy speaking for him, it's his little sister Aryll, who constantly heaps tons of praise on him, showing that she clearly and dearly loves him.
Similarly, Proxi herself is incredibly sweet and supportive to Link and Young Link. She never once sasses him, and it's obvious her encouragement matters to both Links. Especially if you play through the Gerudo Desert as Lana.
Proxi: *after KO'ing 1000 enemies* Link's the coolest, right? Well, I sure think so!
A minor one related to Toon Link, but Tetra has the same chest opening animation as the Hero of Winds. Climbing into the chest is understandable, given their size, but for them both to quickly spin around and show off what they got? It just goes to show how close the two have gotten in theirjourneys together.
While the canon is ambiguous at best, Marin always did want to see the world, but her home's Dream Apocalypse prevented that (unless you manage to beat the game without dying). In this game, Marin can finally see all sorts of places from the Zelda series history.
When Sheik finally reveals her true identity to Impa and asks for her forgiveness for not telling her about it earlier before they have to fight Wizzro, Impa simply accepts fighting alongside her without so much as a word about the whole deception. With Impa's Undying Loyalty towards Sheik's true identity, Zelda, it's quite obvious she won't hold a grudge on her own princess for keeping her in the dark.