Although i love Wind Waker and OoT's music i'm going to say Twilight Princess, the melodies, the remade classics and the original score itself is so wonderfully realised and perfect that it always enthralls me. The remade Zora's Domain sounds incredible, Rutela's theme is superbly fitting, Midna's Desperation is legendary and Lake Hylia is so wonderfully perfect. To me TP is the pinnacle of MIDI, i wish it had been orchestrated, the title cinematic would have been even more epic had it been orchestrated. It was also wonderful to hear tracks from ALttP again too.
Not only that but TP uses its music to really hammer home cutscenes, which isn't something Zelda does much; for example when Link smiles upon seeing midna at games end. Simply wonderful <3