(excuse the spelling/lack of proper names)
Mask Transformations (MM)
Full transformations into a: Deku to spin, use flowers and hop on water. Zora to swim and fight on the ocean floor. Goron to Roll fast, walk in lava and smash rocks. Fierce Deity to own bosses. And many other more subtle effects like running faster, being as noticeable as a plain stone, dancing, marching small animals around and more! Why haven't they used this premise again?!
Free play on the Ocarina (OoT, MM)
Someone figured out how to play the Simpsons theme on this but I can't remember it. In MM the Ocarina transformed into Deku pipes, drums and a bass guitar with mask transformations for different sounds. Let's face it, no other Zelda games have instruments this fun.
Great Bay Temple (MM)
Anyone who has played OoT remembers the Water Temple; the only dungeon that was
easier on the bonus Master Quest game. That's a hard act to follow but Great Bay Temple surpassed it. Link had to navigate an insane maze of pipes by using water spouts, freezing platforms from the water (and enemies) with ice arrows and, best of all, as a Zora.
This is THE best underwater part of the entire Zelda series! I wish more Zeldas would use transformations. Playing Zora Link is awesome!
The boss was okay but the mini bosses were super fun. And to top it off, you could find 15 stray fairies for a defense boost.
Dead Hands (MM, OoT)
Creepiest enemy in the series imo. ReDeads were more common so they got all the creepy credit.
Fun 3D Boss fights
Some bosses were fun to fight even if you knew how and not just the 2D ones. Bongo Bongo and Vovolgia in OoT, Ghot in MM, the Twilit Aquatic/Stahl Lord/City in the Sky Boss in TP, and Lotus dungeon boss (SS) were particularly fun. (only largely overlooked 3D bosses from games I have played are included.)
Arctic Ruins (TP)
Weird dungeon. It was challenging in puzzles and endurance; you took a lot of pain the first time. It didn't exactly 'fit' the Zelda era theme but it wasn't farfetched either. The Soup ingredient goals and haunted but not typical ghost haunted feel added to the mystery.
Tal Tal Heights music (LA)
<3 this music.
(Most) Magic Rods, canes, medallions, cape, and spells (LoZ, ALttP and OoT)
Most of these were only needed for a specific task or a bonus except the Cane of Burma which made useful blocks. They were still really fun and useful but overlooked and not integrated as much as they should have been (think magic arrows in MM). Later games dropped the magic meter all together
. Zelda II did make good use of Link's magic.
Double Clawshots (TP, SS)
As awesome and recognized as the are, they could have been put to a lot more use. There versatile potential was barely tapped and limited to a few vines and obvious grapple points (SS) here and there. They also came so late in the game that few major puzzles needed them (besides City in the Sky <3, TP has the best hookshot/clawshot use in the series with swimming and using them, snagging items etc).
That's all for now.
Keep in mind I only listed underrated and overlooked elements and haven't played many Toon Zelda games.