An alternate interpretation to his death quote can make him feel kind of sympathetic in light of his goals, almost as though, in his dying moments, much like the king, he's realized Link as a hero of a magnitude similair to the hero of time, and realizes that, in some way shape or form, he will bring Hyrule back to life (And he did).
"The wind... it is... blowing."
The above quote can be viewed as a tear jerker or Fridge Horror, depending on which "wind" you think he's referring to. The tear jerker option is the wind that blew through Hyrule— the one he was referring to in saying "I coveted that wind, I suppose"— and it's kind of nice to think that, regardless of what he did, he got to experience it one last time before death. On the other hand, he could be referring to the wind that blew through the Gerudo Valley— the destructive wind. Either is an entirely feasible option since Hyrule has been restored for some small amount of time while Link's been fighting through the castle... but it's also true that Hyrule is pretty much screwed at this point.
In short, this is the only game in the series to really make you feel legitimately bad for Ganondorf, turning him into a sympathetic Well-Intentioned Extremist. It's also the only game in the series where Ganondorf is explicitly killed at the end. Just think about that.
Also in Wind Waker, when Prince Komali arrives to find Medli has left (to become a sage, although he doesn't know that). What makes it worse is when you come back, he's still waiting for her to return, to give her a flower. Come back even later, and the flower's wilted... but he's still waiting.
Link's poor grandmother and her nightmares once you return to her. Accompanied by this music.
The first time you enter the sunken Hyrule Castle, but before claiming the Master Sword. Everything is frozen and grey. The castle is in ruins, overrun by monsters. And that creepy, sorrowful reed music plays in the background.
The statue of the Hero of Time. It's so easy to think of the events of these games restricted only to the space of their specific story, but seeing that statue, the sheer reverence to which his memory is held to, was an incredibly moving moment. For the first time, the Hero's legend was more than just an abstract or reference to a vague history - Ocarina of Time is a story that everyone knows. There's something so hopelessly tragic about rewatching the end of that game, knowing Zelda believes indubiously that she is doing right by Link in sending him back in time so he can start his life over, having no idea of what's to come. It just really sunk in how terribly sad the history behind these games really is.
That statue is later broken. The icon of a beloved hero being defiled like that... It's inexcusable, and tragic, how something so significant of hope can be destroyed so shamelessly.
In the room that houses the Master Sword, the windows are decorated with the images of the Sages that were awakened in Ocarina of Time, showing that their sacrifices were not forgotten by the people of Hyrule. 5 of the 6 Sages had to die in order to fulfil their quest to protect Hyrule, and weren't able to remain in the land that they had given their lives to protect.
They are remembered until the flood, at least, when everyone seems to think that the power of the Gods lies in a special set of eating utensils.
Departure, which only plays two times over the course of the game— both equally heart-wrenching. The first is when Link sets out with the pirates, toward the Forsaken Fortress, waving to his Grandma, and the second... is when Link sets out with the pirates at the end of the game, beginning the search for New Hyrule. The positions are roughly reversed, with Aryll running the length of the dock to wave to him, as they set off.
Speaking to the Deku Tree, where it sinks in that this really is the Hyrule Link saved from Ocarina of Time.
For a more Manly Tears example, when Link pulls the Master Sword from its altar. The music, the sight of that legendary blade, it just brings a tear to the eye.
Related to Skyward Sword's ending, even though by now she may be nothing but residual energy in the Master Sword, this is the last time Fi will ever meet Link "in another life" and is now entombed at the bottom of the sea forever.
Also, when you first find the Master Sword, it's drained of power. Fi is dying.
And finally, when the king refuses to take Link's hand, instead choosing to drown with his kingdom in the belief that, as part of the past, he too should be left behind.
That look of stunned helplessness right after Link runs off a cliff trying in a blinded effort to save his sister. His mind was completely blank except for having to watch his only sister vanish over the horizon and being able to do nothing to stop it.