I don't know what it is... I have this feeling of dread...
One of my favourite moments in the game is when you learn the Song of Time. The setting just works so well, with Zelda appearing in an imaginary Temple of Time, followed by Link as he learns the song. It's a nice moment of calm, especially as it comes immediately after the confrontation with Ganondorf and before vast amounts of plot.
Speaking of Ganondorf, I've just realised something. This is the only Zelda game I can think of where your actions directly benefit the antagonist. Normally Ganon is already part-way through whatever scheme he's plotting and you spend most of the game counteracting this... but here, to succeed all he had to do was sit back and watch as you collect all the Spiritual Stones for him. In fact, the only reason that he was able to enter the Sacred Realm was because you opened the door. Without Zelda teaching you the song, Ruto giving you the Zora's Sapphire, Darunia giving you the Goron's Ruby, and the Great Deku Tree giving you the Kokiri Emerald, the door to the Sacred Realm could not have been opened and Ganon wouldn't have been able to destroy Hyrule - oh, he and the Gerudo would have likely still made a nuisance of themselves, but there wouldn't be ReDeads in Castle Town, a dragon in Death Mountain, or an eternal winter freezing Zora's Domain. There's so many points where that could all have been averted, if only the consequences could have been foreseen.
Ultimately, the destruction of Hyrule is your fault.
This does give a new meaning to the ending - it's not just about letting Link have the childhood that he missed, but it's also about Zelda wanting to fix her own mistakes.
You have led me to the gates of the Sacred Realm... Yes, I owe it all to you, kid!