Tough one.
5. Eclipse of the Sun - Hyrule Warriors
4. Space Harrier Theme - Space Harrier
3. Palace/Temple Theme - Zelda II: The Adventure of Link
While we're at it, I absolutely love this remix of it. Really brings the right vibe for the temples in the game:
2. Megalovania - Undertale
1. Scuttle Town - Shantae and the Pirate's Curse
Honorable Mentions who either just didn't make it, where already mentioned before, or their respective games already had multiple other entries:
Dr Wily's Castle 1&2 - Megaman 2
Jump up, Superstar - Super Mario Odyssey
Mission 1 - Double Dragon
Hell March 1 - Red Alert
Everything from the Parodious series
Main Theme - Arms
Music Type A - Tetris
Baba Yetu - Civilization IV
Monkey Island - The Secret of Monkey Island
Still Alive - Portal
Sloprano - Conker's Bad Fur Day