My favorite dungeon item was definitely the Beetle in Skyward Sword for it was not only used in the dungeon you obtained it in-the Skyview Temple-but throughout the entirety of Skyward Sword. The upgrades were extremely worthwhile as well, being able to wreak devastation by picking up and dropping bombs on enemies or to uncover overworld secrets or simply fetching hard to reach rupees over to Link. Also, the beetle was able to make Ghirahim flinch for a second (at least in the Skyview Temple).
A close second runner-up is definitely the Sand Wand from Spirit Tracks. Not only did it fit well with the puzzle aesthetic of the game's Sand Temple but also proved that an item with few offensive capabilities could be one of the best the series has to offer much like the Spinner from Twilight Princess.
A close second runner-up is definitely the Sand Wand from Spirit Tracks. Not only did it fit well with the puzzle aesthetic of the game's Sand Temple but also proved that an item with few offensive capabilities could be one of the best the series has to offer much like the Spinner from Twilight Princess.