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.
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.
On the villains' 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 CAMPIESTZelda villain in existence.
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 compared to Midna's role 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.
Of the Links, Toon Link has a disproportionate amount of popularity among the fandom due to the perception that he displays more character than any other Link.
Epileptic Trees: Oh, boy! The timeline is arguably the biggest piece of fanon madness in the entire video game medium. Before Hyrule Historia came out to explain it, it was pretty much impossible to find a web site or forums of the series (either fan or otherwise) that did NOT have at least one big article and/or open thread discussing this issue at large, with big, crazy theories to boot. And after it came out, it didn't die. It just evolved into discussing the points that were left ambiguous, debating about the contradictions between the artbook, the interviews to Miyamoto and Aonuma and the games themselves, tiding up the remaining loose ends, or trying to give alternate interpretations to the explanations that were deemed unsatisfactory.
Specially crazy if we take into account that Nintendo put an explicit MST3K Mantra disclaimer in the very same official timeline, explaining that the development team, for the most part, thinks about gameplay first and story later. But fans still treat this topic as Serious Business.
Escapist Character: Part of Link's popularity as a character stems from this and how players can, in addition to wishing they were him, largely project their own personality onto him as he's a Heroic Mime.
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.
Since the timeline was an endless fountain of Epileptic Trees for over a decade, many fans disliked those explanations which invalidated their own theories.
Fan Wank: The endless, endless confusion over "the timeline," something officially confirmed, but NEVER officially explained. Even after Hyrule Historia explained it all, it's still going, even if discussing different points (See Epileptic Trees above).
Germans Love David Hasselhoff: While wildly popular elsewhere, the Zelda franchise isn't quite as popular in its native Japan (but still popular).
Goddamned Bats: An early example, though Keese and Fire Keese are hardly the only ones.
It's Easy, so It Sucks: A common complaint about entries after the N64 era among veteran fans, specially those who grew up with the firstthreegames. The Wind Waker is arguably the worst offender (albeit the Hero Mode in the Wii U HD version fixed it in the eyes of many).
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.
Yahtzee even managed to do both in one review, bashing Skyward Sword for being formulaic, then for not holding to its own formulas.
Memetic Loser: Tingle is a 35 year-old man who dresses in a green onesie and wishes to become a fairy. He's meant to be a Man Child and is loved by the Japanese fanbase... But the Western fanbase love to loath him. When you have a trope called "Americans Hate Tingle" named after you, you know you're a memetic loser.
Older Than They Think: The completed Triforce is actually a Christian symbol representing the Holy Trinity (because it's one unit and three at the same time). It was appropriated around the same time the series moved into original mythology territory and away from being a Christian allegory, and so was reinterpreted as a trinity of goddesses.
Scapegoat Creator: A lot of fans blame Eiji Aonuma, the current main producer of the series, of every single thing that is supposedly wrong with the series nowadays. Of course, when they see something that goes right for them, then they praise Miyamoto for it. Classy, isn't it?...
Shipping: A rabbit hole that runs too deep to get into right here.
Sidetracked by the Gold Saucer: Each game is bound to have at least one sidequest or minigame that completely distracts from the main story. In fact, some games make the story seem like a minor annoyance than a matter of importance in the game.
Vindicated by History: Actually a recurring element. Since Majora's Mask, every time a new console game is released, it's immediately panned by the fans while the previous title is suddenly favored.
Writer Cop Out: The addition of the "Link is Defeated" timeline is seen this way by many, since it turns that part of the timeline into a "What If?" scenario instead of having a stronger explanation involving legitimate and certain events that lead up to the defeat. Not to mention that it opens up the question of why there aren't other timelines created by "Game Overs" in games of the series other than Ocarina of Time.