Gerudo Valley was AMAZING. I also like the Medley, especially when they started playing the Dark World theme from ALTTP, one of the best tracks in Zelda period imo.
I really like the Wind Waker movement! It felt good to relive the music of the small portion of the first Zelda game I played before my sister broke it. I never even got very far...
Twilight Princess seemed...kinda dark for me, haha. The others are great too, second favorite being a tie of Ballad of the Goddess and the 25th Anniversary Medley. Ballad of the Goddess is just so, grand and beautiful, and the 25th Anniversary Medley is just pure remembrance of music throughout Zelda.
Gerudo valley... made me think of the women pirates who were always able to detroy my self-esteem by throwing me in jail and saying i was a stupid un-needed man.