Ooh, this is my wheelhouse because I am a musician.
Probably the Spirit Temple theme from Ocarina of Time in terms of what interests me as a musician and speaks to me.
Now, let me tell you this deserves more love than it gets.
First of all, it utilizes what I call "the dark scales of metal."
The start of the theme starts off in straight G Phrygian.
But the rest of the melody floats in between three tonalities, that nobody ever correctly covers.
Because of the key itself (G minor), and the tonality (G Phrygian) there's going to be lots of accidentals, but if you play straight G Phrygian, it doesn't sound right.
That's because it floats to G Phrygian Dominant too, which has a major third, instead of a minor third, like G Phrygian.
And for a bit it'll stray into G Double Harmonic, sometimes known as the Byzantine scale, or I've heard it called Super Turkish, which sounds like a coffee, because I hear that clear leading tone if only briefly.
Overall it creates a dark and exotic feel, which is appropriate for the setting.
So that means in one composition, we're mixing in three different, yet somewhat related tonalities, giving it that flair that it needed.
I could actually analyze Zelda music all day, because you will find some interesting musical quirks, such as Ganondorf's Boss Battle theme in OoT being in the time signature of 15/16, Midna's Lament from Twilight Princess being in 6/8, or creative use of rhythm in the Forest Temple's theme in OoT sounding like bone rattles, or Majora's Theme containing a lot of tritones.
But in terms of my favorite theme overall?
The Dark World theme hands down. This is majestic and powerful.