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.
The entire sequence with Boomer in the return trip to Bowser's Keep. Boomer is some kind of robot samurai, who challenges your party to a duel in Bowser's throne room as though you were his sworn rival... despite the fact that he'd never even appeared in the game up to that point or even been hinted at. You battle him atop the chandeliers in an homage to the first boss fight in the game, and when you defeat him, he commits suicide by cutting the rope of his chandelier while lamenting his defeat in completely overwrought tones. Following this, the Shyguy holding up your chandelier lugs you up to the top of the Keep while jaunty music plays and your party members dance a jig. The whole sequence comes completely out of nowhere and is never explained or mentioned again.
A minor one: after hitting a switch in Booster's Tower, a new area opens up in Booster Pass. Here you can fight an apprentice Snifit who wants to join Booster's entourage. After you crush his dreams by beating him in a fight, he's never seen again.
Unless you somehow get defeated by him. Then you can see him in Booster's Tower as the 4th Snifit.
But in the ending 8 Snifits attend the Wedding, so Booster's wedding bliss must have changed his mind.
There's also the whole sequence with Bundt, a cake that comes to life for no reason whatsoever and you have to fight it.
Breather Level: Star Hill. It's a pretty short area where you find a Star without any interference from the Smithy Gang or any boss fight whatsoever.
The original player's guide even calls the star you find here a reward, after all the trouble you went through in Booster's Tower and Marrymore.
It makes up for the fact that you're going to have to earn the fifth star twice, and the second time is from That One Boss.
Critical Research Failure /"Blind Idiot" Translation: This game's American translators were so unfamiliar with the series that they gave different names to iconic enemies. These include Sky Troopa (Koopa Paratroopa), Goombette (Microgoomba), Goby (Cheep Cheep), Shy Away (Beezo), Chompweed (Nipper Plant), The Big Boo (a small Boo). Also, Wigglers are supposed to have at least eight legs, not six.
Also, Yoshi's Island is known in this game as Yo'ster Isle (it is known as Yoster Island in Japan for this game and Super Mario World).
The translations for a few of the enemy spell names are also weird, in particular the "drain" series. Drain's original name was fireball, though renaming it drain can be forgiven since the spell does have an hp-stealing effect. Mega drain and drain beam, however, do not have an hp-stealing component, and their original names were light saber and geyser respectively.
This even extends to some of the weapons. The NokNok Shell should have been the Koopa Shell (Koopa Troopas are called Nokonoko in the Japanese).
Cult Classic: Regarded as such, especially in the United States. The SNES game did receive critical acclaim, but its success was limited there because the Nintendo 64 was released four months later.
Ending Fatigue: In Bowser's Castle, you have to go through 4 long hallways, which consist of either difficult jumping puzzles, a TON of enemies, or normal puzzles. Without saving in between. And of course, it's only the next-to-last dungeon. Even Bowser is willing to call it quits afterward.
What's worse is 4 of the 6 doors contain the ultimate weapons for the majority of the party, so if you miss any of them, you'll be forced to finish the rest of the castle and then come back and go through the trek of getting to the 6 doors again to try again.
The items are not randomized, though. They're always behind the same paths.
Nimbus land is also noticeable for having Ending Fatigue, as it's crammed full of enemies, difficult jumping puzzles, and gives you no real reward for completing besides plot advancement.
Foe Yay: Play your cards right in Marrymore and you can get Bowser to kiss Mario!
In the same scene he asks Toadstool for a kiss when she promises one to Mario for rescuing her.
Fridge Brilliance: Smithy is ruler of another world, uses a hammer as his weapon, can shapeshift, and with the four members of the gang besides Exor (counting the Axem Rangers as on entry) he leads a Five-Man Band that seek the Star Pieces...could Smithy have been intentionally designed as an Evil Counterpart to Mario?
Smithy is a blacksmith, Mario is a plumber. Hmm...
The similarities go further: Both of them sport awesome facial hair of some kind (Mario a mustache and Smithy a beard).
Without the Star Road, no one's dream can come true. That also includes Smithy's wish of ruling the Mushroom Kingdom.
The scenes with Gaz and Geno parody Fixer Sue with how Geno usurps Mario's role and how Gaz treats his custom doll with more respect than Mario. Geno (or rather, the spirit inhabiting him) is wildly popular, reasonably developed, and useful on the front lines, which is a welcome bonus.
While the mass produced Machine Made copies of Smithy's lieutenants have some improved stats over the originals, they are of overall lower quality than the originals and tend to go down faster as a result. In real life it's a common belief (sometimes justified) that mass production tends to result in lower quality products.
Toadstool. With a Timed Hit, her Group Hug spell will heal enough HP to likely restore everyone to full and also heals status ailments, for a measly 4 FP. Then she gets Come Back, which revives a party member at full HP with a Timed Hit. Add in the Lazy Shell and Safety Ring to boost her defenses and she's nearly unkillable. And her ultimate weapon is one of the best in the game and allows her to hit just as hard as Geno or Bowser. Having her in the party makes you pretty much invincible unless a group of enemies concentrates their fire on her, or a really powerful group attack kills everyone at once.
Geno, plain and simple. His Geno Whirl attack timed hit does 9999 damage each time for a small amount of flower points. No, seriously it does that much damage when timed correctly.
Geno's magic attacks are the most powerful in the game. For a while, Bowser is more useful to the team than him, but by the end of the game the best team to use is by far Mario/Toadstool/Geno.
The Work Pants are arguably more useful than any armor you pick up afterward. This is especially the case for Bowser, as it provides better defense than the any of his armors up to the Barrel Volcano store, provided you had the foresight to equip him with one, as he shows up after you've completed Moleville.
Using the Quartz Charm or the Jinx Belt (Received by Culex and Jinx respectively) on a character makes their stats boost up to insane levels. In addition the Quartz Charm makes you immune to all status effects including instant death, so if you put this on Princess Toadstool well, you can see where this is going.
The Safety Ring and Safety Badge. Both prevent all status effects and aren't hard to get (though one is in an out of the way place). The Safety Ring however, also makes one immune to all magic and instant death attacks. If you're good with timed defenses, the character equipped with this pretty much has no trouble staying alive.
The Lazy Shell and the Lazy Armor. The Lazy Shell has the highest physical damage output with a timed hit in the entire game, while the Lazy Armor turns whoever wears it into a Stone Wall who probably will never faint unless you're really unlucky. Also you can attach this armor to anyone, including Princess Toadstool.
In the process of doing this, you'll earn the Attack Scarf for Mario by doing 30 Super Jumps. Put both of these items on Mario and his speed stat will be so high that in the fight against Culex, he'll get a turn before Culex's monologue!
Nightmare Fuel: The final battle with Smithy. Never mind that he hammers his own skull into new weapons; he's a massive war machine in a playful fantasy world.
Scrappy Mechanic: The flower points system which act as your magic points are all shared between your entire party instead of character having their own specific and individual amount of magic like in most RPG's.
Squick: Would eating rotten mushrooms in the middle of a fight induce vomiting or healing, do you think? And how gross do you think the inside of Belome's mouth is, especially after having recently eaten your teammates?
You will come to dread some certain attacks as you continue your quest to a point seeing its name on the text box before its execution will be enough to invoke This Is Gonna Suck. Such as Sand Storm, a strong attack when you first experience it that not only deals considerable damage to your entire party but also induces the Fear status, which cuts offense in defense in half.
Yaridovich's Water Blast move is multi-target and hits like a truck even if your party is decently-levelled when you face him. It's not uncommon for the battle to be going swimmingly until Yari pulls this and causes a Total Party Kill. And did we mention it's Non-Elemental, so the Safety Ring won't protect you from it?
Multistrike is a multiple hitting attack that is extremely powerful, and can take most characters other than Mario or Bowser down easily in one or two uses unless they have really good armor. Later on many enemies and even bosses will spam this attack over and over again, which makes it that much more dangerous and irritating.
Dark Star is the most powerful special an enemy can have and easily scores triple-digit damage even on a high-leveled, fully-armored player. At least unlike the move it's based on (Mallow's Star Rain), it only targets one character.
Bundt; a living cake that can debuff and possibly wipe out your whole party with one magic attack, and regenerates itself.
Yaridovich can also prove to be quite the challenge with Water Blast and his ability to clone himself.
As long as Toadstool can survive a water blast at full HP, he's pretty much a piece of cake. Doubly so with Mallow in your party, since Yaridovich is both vulnerable to lightning and Psychopath can reveal which clone is fake (or you can just use Thunderbolt to hit both of them; the real one takes less damage).
You don't even need to do that. When you input your attacks, the cursor always defaults to the real Yaridovich.
The second time you fight him, Belome can create clones of your party members, and puts your entire party to sleep.
Bowyer, so much. He has the ability to temporarily shut off your actions, and will keep shutting off your attack ability until you run out of magic points, and continue attacking until your health is extremely low. Only through extreme patience could you defeat him easily.
The first fight against Croco is pretty bad if you're underleveled and caught off guard considering that you only have two characters to fight with at the time.
Also, the second battle against Croco. After depleting some of his HP, he takes all your items away. Hope you didn't waste all your FP!
At lower levels, Birdo can be quite frustrating as well, since an unguarded egg will basically KO any party member under level 13, and almost every direct attack will do single digit damage to her...
Queen Valentina and Dodo also count. They're formidable together, but things get even worse when Dodo takes your middle character to fight one-on-one, and if your lone character loses, the game is over. Considering the fact that Dodo has an attack called Multistrike which pecks you multiple times for huge damage, and that he can take you down with two or three of these attacks, while he has decent health and defense, this becomes a big problem really quickly. Heaven help you if you happened to put Toadstool or Mallow in the center-slot. On the up-side if you lose you know better for the rematch, but Dodo is still pretty tough no matter who you send against him.
Barrel Volcano has Those Three Bosses (Czar Dragon, Zombone, and the Axem Rangers) back to back - though you can at least save after the first two if you know what's coming.
That One Sidequest: Speak to a particular Chow in Monstro Town, and it will tell you how many Super Jumps you've managed to make in a single use of the technique. What some players never realize is that you can go back and receive an extremely handsome reward if your record hits 30 Super Jumps, and a much, much better one at 100. This requires perfect timing, rock-solid concentration, and lots and lots and lots of practice.
The Woobie: Many characters count for this, but Mallow really stands out in this area. It rains when he cries. Which he does. A lot.