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.
Breather Boss: Arrghus is not only a much easier boss than the Helmosaur King, but arguably even the easiest boss in the game overall.
Depending on your strategy, Mothula could be either this or That One Boss. The boss is vulnerable to almost any attack from any angle and dies fairly quickly.
Breather Level: Thieves' Town (Blind's Hideout). It is MUCH smaller and shorter than all of the other Dark World dungeons. The only difficult part is the boss.
Epileptic Trees: Like every Zelda game, this one had a debated place in the timeline before its official release, not at all helped by the ending line of "The Master Sword sleeps again...forever!" Despite the fact that, at the time, there were only two places it could possibly go: either before the original game, which was what ended up being the case, or after the second game.
Game Breaker: The Cane of Byrna makes you invincible and simultaneously deals damage to enemies. Most experienced players contend that "Only wimps use the cane."
The Magic Powder's ability to turn Anti-Fairies into Fairies probably qualifies.
Speed Runs make heavy use of the Pegasus Boots and the fact that Link flies a few tiles backwards through the air after running into a solid object. This allows players to cross gaps that would normally require the hookshot or some other item.
That feature was used in at least one place in Ganon's Tower, intentionally, in the form of ramming into a wall to fly backward across the gap to get to the entrance of a room on the other side. (The only Hookshot point across the gap is when coming from the side that is accessed by using the Pegasus Boots trick.) It was either that, or use bombs on oneself. Regardless, this room is completely optional, as it only contains several Rupees and is not required to progress.
Goddamned Boss: Moldorm might not be the toughest boss in the game, but he's easily the most frustrating one, simply because he has a completely unpredictable pattern and can knock you off the edge of his platform, forcing you to restart the battle. Worse still, if you attack him but fail to hit his weak spot, that also sends you flying backwards.
Mothula, where the biggest hazard is not the boss itself but the whirling spikes on the floor under it.
Good Bad Bugs: Rarely mentioned - The Hookshot renders you invincible while its extended. Attacks either pass through you or hit with no effect. Very useful against those pesky Beamos.
Growing the Beard: This game is often considered to be this for the Zelda franchise, as it was the first to set the series' formula into gear and introduce more intricate characters and deeper lore for the series.
As for in the game itself, after Agahnim warps Link to the Dark World is when the game starts to become truly epic.
Hilarious in Hindsight: The original Shotaro IshinomoriNintendo Power comic adaptation is practically prophetic when you look back on it now. Link has a fairy companion, the magic of the Dark World transforms him into a wolf (instead of a rabbit), and Zelda is the one to kill Ganon by shooting him with the Silver Arrow.
That One Boss: The Helmasaur King is very frustrating, mostly because you face him at a point in the game where you have relatively few upgrades, and probably only six or seven heart containers. The latter becomes an even bigger problem when you take into account the fact that he has an attack which drains a full heart container, and can be difficult to dodge, especially if he uses it and his other attack at the same time (he often does).
Mothula: Not only is his movement pattern random and diagonal, but the floor keeps moving to send you into spikes. While the boss spits fireballs at you.
That One Level: The Ice Palace, which is full of some of the game's strongest enemies, has a ton of rooms filled with slippery floors, and requires you to double back on yourself twice in order to defeat the infamous "Block-Switch" puzzle. Many players skip over to the following Misery Mire dungeon in order to obtain the Cane of Somaria, which nullifies the aforementioned puzzle — and the fact that so many players are willing to delay getting hold of the Ice Palace's armor upgrade to skip the puzzle should tell you everything.
Skull Woods. Not that bad on its own...but if you die during the outdoor segments between entrances and exits? Good luck walking all the way back! Oh, and there are these new enemies you haven't seen yet in any level 'til now called Wallmasters. Have fun!
Unwinnable by Insanity: It's possible to glitch your way into the first battle with Agahnim immediately after you rescue Princess Zelda right at the start of the game. If you beat him however, then you get transported into the Dark World — which is a very bad thing since you won't have either the Magic Mirror or the Moon Pearl, meaning that you instantly turn into Bunny Link, can't return to the Light World, and can't do a thing in the Dark World beyond wandering around until you eventually get killed.
Woolseyism: The Book of Mudora in the Japanese version was treated more like an instruction booklet for what Link can do. The English version translated it in such a way that made it seem as though it contained various myths and prophecies, and worded the instruction in such a way that did seem somewhat prophetic.