@Felthry This may be recency bias, but Zelda 2: Great Palace.
Z2 is not my favorite game in the series, and other dungeons have my favorite mechanics and gimmicks in the series (TP Arbiter's Grounds is also high on my list, as is LA Eagle's Tower), but providing a sprawling, non-linear dungeon at the end of that adventure with one of the most iconic non-Ganon fights in the series had a significant impact on me (both when I first played it and more recently).
It also remixes very well in rando.