These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Blue Wizzrobes. They do major damage, they're durable, they have an incredibly hard to predict motion pattern and you can't stand in front of them because they continuously fire spells if you do.
Blue Darknuts. They can't be attacked from the front, they're twice as fast and durable as Red Darknuts, and they do major damage.
Like-Likes. They eat your Magic Shield.
Good Bad Bugs: In both the NES original and the GBA edition, immediately exiting and reentering the Level 1 dungeon will somehow unlock the first door, netting you a spare key. Hard to tell if this is an unintentional bug or a deliberate secret, though.
Broad Strokes: The continuity certainly is this, moreso with the more recent console games as they generally have more continuity nods than the other games.
Zant, first and foremost for executing Queen Rutela as a warning for the other Zoras, not to mention turning his own people, the Twili, into monsters to help him conquer Hyrule.
Ganon's referred to as the King of Evil for a reason.
Of course. The Wind Waker made him a little bit more sympathetic.
Ghirahim.
Contested Sequel: ANY of the console games that follow up on Ocarina of Time, there's no arguing against it. Skyward Sword has even become this before it has even been released!
Die for Our Ship: Anything that threatens the possibility of a Link/Zelda pairing is violently purged. Zelda herself can suffer this when other choices are available. (Ocarina of Time, Twilight Princess)
Dork Age: The CD-i games. Their sting wasn't numbed at all by the fact that Nintendo took its sweet time developing Ocarina Of Time, so there were five years between 1993 and 1998 when no Zelda games except for those were being released.
And on the villain's side we have Dark Link, who has appeared in all of four games and yet is one of the most popular characters. Also, Vaati, villain of all Four Sword-related games. Many fans want him to make an appearance in a main console game. Then there's Ghirahim of Skyward Sword, who's possibly the CAMPIEST Zelda villain in existence.
I AM ERROR.
In Japan, Tingle falls under this, getting no less than two of his own games.
Malon has quite a fan following to her name. As far as female Zelda characters go, she was probably second in popularity to Zelda before Twilight Princess came out, and Malon's popularity could be considered more impressive given her much smaller role in Ocarina of Time comparison to Midna in Twilight Princess. She probably got even more popular after Twilight Princess, in which the game's Link is a rancher, leading to many to theorize that she and the Hero of Time got together.
Fan-Disliked Explanation: As explained in Hyrule Historia (a guidebook about the franchise by Nintendo), there is a third timeline that also split from Ocarina of Time. The problem is that it is based on an event that didn't happen anywhere in the game: The hero dying. And no, Game Overs do not count.
Fan Dumb: Every time a new zelda game is announced, it's automatically the "Worst game in the series". The previous game, which used to hold that title of "Worst game in the series" is now suddenly praised and beloved. This was especially prevalent with Wind Waker and Twilight Princess, but it dates as far back as Majora's Mask.
Fan Wank: The endless, endless confusion over "the timeline," something officially confirmed, but NEVER officially explained.
It's the Same, Now It Sucks/They Changed It, Now It Sucks: Every single entry of the series ever since Ocarina of Time (if not even earlier than that) has received both of these at the same time. One second you find a comment trashing the game for not changing the Zelda formula at all, demeaning its new features as "gimmicks", and the next second you find another one that trashes it because those "gimmicks" are new features that totally change (and ruin) the Zelda formula.
Sequel Displacement: Most of the series' current fans came in after Ocarina of Time and it was surprisingly common to see Majora's Mask referred to as "Zelda 2," even though the real Zelda II was made ten years before Ocarina.
Shipping: A rabbit hole that runs too deep to get into right here.
So Cool Its Awesome: There's a reason why this is one of Nintendo's flagship franchises and one of the most respected series in the entire video game industry. Even at its worst, no Zelda game is less than stunning.
That One Level: Arguably every water dungeon in the series.