For me it has to be two tracks, and those tracks are "The Last Array" for its incredible brass! And the other track is "From the Union". I gotta say when fighting the final progeny that track just makes it all too thrilling, even though the boss can be easy.
EDIT: Feel free to post other game sound track pieces if you like them. A good example is "Those who get in our way" in Xenoblade Chronicles. Awesome track
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The entire Majora's Mask soundtrack.