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.
Anti-Climax Boss: Ganon. He's slow and predictable, and he doesn't have a second/third form like the two vanilla final bosses and the boss that comes before him. Some of it is justified, but it's still a bit jarring for the former King of Evil.
Breather Boss: Plasmarine, boss of Jabu-Jabu's Belly in Ages. Really easy to dodge, has only two attacks, and one of them is incredibly slow-moving. Considering that level's reputation among the fandom, it also counts as a Hard Level Easy Boss.
Crowning Music of Awesome: For a handheld game, the final boss music for both games counts. Onyx, with his dragon/wyvern form, arguably pulls it off better.
The Tarm Ruins from Seasons is a suprisingly mellow and melancholy song that many people remember.
Meanwhile Dancing Dragon Dungeon, also from Seasons, is just so damn funky.
Disappointing Last Level: The Black Tower in Ages isn't exactly an awesome dungeon, but it is a dungeon with a couple of puzzles and a long path. Onox's Castle in Seasons, on the other hand, is barely a dungeon at all. The level consists of three wide-open rooms, you walk up, beat the enemies, walk up, beat the enemies, walk up, beat a miniboss, walk up to find Onox's room. The fight with Onox will likely take far longer than the time it takes to get to him.
Evil Is Sexy: Veran.◊ As you can clearly see, Veran reads like a scrolling laundry list of kinks, and then some. Even two of her One Winged Angels forms (her true appearance as a fairy and her beetle transformation) are Cute Monster Girls, although they do veer a bit toward the creepy side.
Fridge Brilliance: In "Seasons," the Maku Tree is unable to see the location of the final Essence of Nature in his dreams. That's because it's not in Holodrum—it's in Subrosia.
Game Breaker: The Red Ring in Seasons doubles all sword damage. This makes any normal attack a Spin Attack and Spin Attacks do quadruple normal damage. Combine it with the Master Sword in a linked game and Spin Attacks reach 12 power. Even the final bosses of the games will die in a few seconds. This explains why so many late game bosses and minibosses are immune to sword strikes or are Puzzle Bosses.
Goddamn Keese: More obnoxious in this incarnation than in most others. Especially the flaming varieties.
Goddamned Boss: The second boss from Ages. You must sit on slow moving platforms that rotate above his head so you can drop bombs into it. Then you must wait for him to stop spinning and hope that the bomb lands while the boss has a Red face. All other faces will cause him to counterattack, knocking you off the platform. All of this eats up a lot of time. If you're patient though there are plenty of safety spots to hide in and if the bomb hits when he's on the Red face he will always land on red. But yeeesh.
The Head Thwomp is much easier when you realize that A: the game certainly expects you to use the rotating platforms, but you can stand on the fixed upper platforms and still toss bombs into it just fine, and B: it's not based on luck, but timing. Throwing the bomb in just as his face turns purple will always cause it to land on Red.
Guide Dang It: In Seasons, you are very likely to forget that autumn also fills in certain holes with leaves. You need to do this once in order to get to the 8th dungeon. This even threw off the official guidebook, which advised you that you needed to try and jump the gap with the Roc's Cape, a virtually impossible feat.
Marathon Level: The Ancient Ruins from Seasons are a strong contender for the longest level in a handheld Zelda game. It doesn't help that Manhandla, the boss, is considered Season's That One Boss.
Scrappy Mechanic: The two Pieces of Heart you get from a Gasha Tree and Maple. It is completely random when these pop up, so prepare to spend a long time trying to get those.
Swimming in Ages after you get the Mermaid Suit. You have to mash the D-pad for an entire dungeon. To counterbalance that, it's fast (much faster than mashing A with the flippers) and lets you use your items.
Stop Helping Me!: Ralph. He'll give hints, but more often he just nags Link for wasting time helping other people instead of trying to save Nayru.
Take That, Scrappy!: Ricky can't stand to be around the creepy man-child, Tingle. The kangaroo will leave Link if they go anywhere near him.
That One Boss: Smog, also in Ages, for being a particularly frustrating Puzzle Boss. What doesn't help are the projectiles he shoots that can easily deal a great amount of damage if you're not careful.
The Ancient Ruins boss Manhandla, a giant Venus flytrap that shoots fireballs. Sounds easy enough, except that: you need to take out the heads with the boomerang, the heads are only vulnerable when they're shooting at you, the boomerang averts the "precise" part of Precision-Guided Boomerang when you're trying to guide it around (the heads are on all four sides), the boss gets faster with every head destroyed, you use the same buttons to move as to control the boomerang (making you a sitting duck), and, adding insult to injury, there are conveyor belts on the floor that pull you into the boss if you step on them (see: same buttons for movement and boomerang). Good thing you found that Quicksand Ring a while back,right?
The Goron dancing minigame in Ages, because it's so easy to screw up the timing. What makes it worse is that it's mandatory to complete the game. Not only that, but doing the dancing minigame in the Past can fail to give you the key to the Mermaid's Cave in the Past, rendering the game impossible to complete!
Jabu-Jabu's Belly, seventh dungeon in Ages. It's a goddamn maze in there, to solve certain puzzles you have to navigate and backtrack through a dozen times, and being as it's inside a giant fish at the bottom of the ocean, you have to use the Mermaid Suit to get around.
The eighth dungeon from Ages has an underwater sequence with quicksands. One particularly tricky part is almost impossible without the quicksand ring.
That One Sidequest: The Hero's Cave in a linked game. In an unlinked game, it's just a short dungeon in Seasons that you go through to first get your sword, and it doesn't even exist in Ages, but in the linked games, it's 21 rooms long in Seasons and 15 in Ages and in both cases you need to have the equipment from the 7th dungeon in order to clear it.
The second-to-last puzzle in Seasons is hair-pullingly hard, because you need to perform a very precise boomerang throw to hit a switch. And the boomerang is FAST, which mean you need a hell lot of reflexes to pull it off. However, you can circumvent that puzzle by using Pegasus seeds to control the return path of the boomerang in such a way that it goes through the blocks and hits the switch on the way back. Bombchus work too.
Then there's the dice puzzle in Ages. You have to push a colored dice over three color tiles in a room filled with lava. You can cool it down by pulling a lever, giving you only a few seconds to push the dice from one safe area to the next. If the lava starts to boil again while you roll the dice over it, you lose it and have to exit the room and start over from the beginning. To make things worse, you access that room through a warp vortex, and if you fall into the lava, when you re-spawn on top of the vortex, it immediately warps you out of the room, forcing you to start over even if you didn't lose the dice. There really aren't much room for mistakes.
A few of the linked game mini-games can be this. With seasons being the first game you beat, cutting grass with the Magic Boomerang in just 3 throws. With Ages as the first, the one that stands out is doing the sword batting cage mini game WITH THE BIGGORON SWORD.
The Goron Dance on Platinum level requires up to 10 precisely timed button presses, and you have to do them perfect all eight times in order to get the Bomber's Ring, and there is no other way in either game to get it. The 3DS virtual console release inadvertently makes this much easier by allowing the player to make restore points during the dance between rounds, so you can just save scum until you nail it.
Unwinnable: In Ages, completing a certain minigame in the Past can fail to give you an important item necessary to complete the game. See That One Level above.