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.
Not just the boss themes; most of the soundtrack qualifies. While Secret of Mana is usually regarded as Kikuta's masterpiece, truthfully the music from this game isn't very far behind.
Demonic Spiders: Near the end of the game there are a number of enemies that are essentially the mook version of some of the playable characters' final classes, and each of them can utilize the tech that the player class has. For example, the Nightblade can use Split-Image Slice (like Hawk's Nightblade class), and the Bloody Wolf can use Suzaku Sky Dance (like Kevin's Dervish class). These techniques are full-screen and can easily wipe out the entire party if they are at low health. This is a significant contributor to why fans are so fond of the Star Lancer and Night Blade classes, as both have the ability to silence enemies, preventing these attacks from being used.
Others include the aptly named Death Machines and nigh unbeatable packs of multi-healing Silver Wolves.
Even Better Sequel: To Secret of Mana, arguably. The game improves on the original game's graphics and mechanics and manages a soundtrack of comparable brilliance with even more songs. It's also longer and it far outstrips its predecessor in terms of replay value due to the fact that it takes at least three playthroughs to see even most of the game's content, and the presence of six playable characters and the class change system introduces literally thousands of possible final party combinations. There is a sizeable contingent of fans that regards this games as one of Square's finest achievements during the 16-bit era.
Fan-Preferred Couple: Even though Hawk already has a "girlfriend," many fans prefer to ship him with Lise. Their stories are related to each other and it doesn't help that the game put in some minor Ship Tease in there (nor does it help that Hawk's "girlfriend" basically has zero screen time). This was strengthened when Heroes of Mana revealed that Hawk's "girlfriend" is his mother's half-sister.
Fridge Brilliance: The scene with Lugar and the defeated Altenan sorceresses is a good clue about the types of attacks you want to avoid using when you fight him.
Also, putting the final classes in context with the back-stories of each character really increases their significance. In most cases, the Light classes are more based on duty and/or idealized versions of certain figures in their lives, while the Dark classes are more based on obsession and/or the actual current situation of said figures.
For example, Duran's Light final classes, Paladin and Lord, seem to be based on his father Loki as a Knight of Gold. His Dark classes, Sword Master and Duelist, reflect the current situation of his father actually being the Darkshine Knight. Also, an early plot point in Duran's story is how he wants to learn magic so he can fight Koren on an even standing. Aside from Saint Saber, Duran can only learn sword magic if he goes Dark.
Carlie might even be a case of Break and then Corrupt the Cutie if she goes dark. Think about it, she's so madly in love with Heath, who is Brainwashed and Crazy thanks to the Masked Mage that she would walk down the same path as him WILLINGLY just to be with him. Her final light classes on the other hand, are essentially Carlie choosing which of her grandfathers she'll emulate.
Kevin's duality is more based on his human side with his Light classes, or his beastman side with his Dark classes.
Hawk's classes take a different spin of this trend: keep in mind that the Desert of Scorching Heat was once a huge forest: the Wanderer and Rogue recall that time, while the Ninja Master and Nightblade reflect the reality of things.
Angela's Light classes seem to reflect a desire to emulate her mother, while her Dark classes are more based on her pursuit of magical ability like Koren.
Lise's Light classes seem to be based on her motherly instincts, while her Dark classes may be more based on her role as warrior princess.
Accessing the menu while charging up a spell will make the spell charge when you are in the menu and the game is paused, meaning you can technically rapid-fire all of your spells without worrying about being interrupted. (The enemies charge their spells while you're in the menu too, however, so it's not completely game breaking.)
Arguably using Hawk and Kevin in the same team since they have double attacks. (Or really pretty much everything Kevin does.) Oh their FIRST skill (green bar) can be STRONGER than their last (red bar) when buffed with elements and Power Ups. If you picked their "darkest" classes (Nightblade for Hawk and Death Hand for Kevin) they tear even bosses apart. Add some more pain if you lower the enemy's defenses.
Counter Magic or Matango Oils (which has the same magic effect) render most of Koren's spells useless. It's only a game breaker in that one fight but it's still fun.
There are some who consider Byzel's black market a Game Breaker itself, as the items purchasable potentially render many classes almost entirely redundant.
While Silver Wolves aren't terribly dangerous on their own, they just love to spam Heal Light, and also have a move that severely reduces your attack power. If you don't have a way to boost it back up and/or lower their defense, you're going to be fighting them for a long time. Or not, if there are Bloody Wolves around too.
If you choose Carlie or Kevin as first characters, much later in the game, you have Death Machines which almost always reduces the entire party's defense making even weak enemies dangerous and stronger ones downright mortal.
Good Bad Bugs: Some of the Standard Status Effects (specifically: Poison, Moogle, Chibikko (shrink), Petrification, and Silence) don't stack with one another - the most recent one takes precedence. During the course of the plot, you get an item called the Chibikko Hammer, which either inflicts or cures the Chibikko status on your party. So, if a party member gets hit with one of the other statuses, two hits from the hammer (once to Chibikko them, and once to cure it) will get rid of it without having to use any status curing items or spells.
It's not clear whether it's intentional or not, but the Evil Shaman's AntiMagic spell will, in addition to dispelling status buffs, cause enemies that absorb certain elements to no longer do just that.
No Export for You: Far and away one of the most infamous examples in video game history; a translation was in the works, the game was even advertised briefly in Nintendo Power and elsewhere as Secret of Mana 2... and then Square decided to shift development resources elsewhere, to things like Secret of Evermore and Super Mario RPG. A lot of fans are still bitter about this, and worse, it is now the only major World of Mana game to never get an overseas release (even its prequel got one).
That One Boss: All of them have tendency to counter any spell or high level technique with their own specials.
Bill and Ben, Lugar, and Darkshine Knight all qualify. To put it in perspective, Darkshine Knight will counter offensive magic (and conveniently enough one of the two who have to fight him is a mage) with a full-party hitting attack. He can also pull them off without getting provoked. Two of these in a row will destroy your party unless you're over-levelled.
Lugar during the first visit to Mooreading Tower may come as a nasty surprise to players who likes to abuse Level 2 Techs. He reacts to these techs with one of his own and once he closes to death he starts using all-party variations of said attacks and potentially in succession if the player is careless meaning he can cause a party wipe faster than a recovery item can be thrown.
Dolan and Zable Fahr are considered the most difficult of the 8 God-Beasts. The former because aside from his all-round power, has a strong attack the temporarily reduces the party's max HP in addition to inflicting massive damage. With the latter, it has really strong attacks in addition to hitting the party with de-buff spells, and has the instant death spell that will kill a party member they are at a lower level than it, and odds are they will be. Thankfully, Zable Fahr has fairly low HP. Even the final class change of the game comes right before the battle, Zable Fahr is still regarded as the hardest of the God-Beasts.
Heath. Oh damn, Heath is a nightmare! Most fans agree that even if the Dark Lich is easiest Final Boss, he's the hardest penultimate boss. Not only is he a cross-class cleric/mage, he has improbable amounts of health (as his name implies), he knows debuff spells against your entire party which render your fighters invalid, can heal and knows all darkness spells, all light spells AND 3 of the 4 possible summons for Liese, which are all party-wide heavy damage in addition to inflicting mute (Marduke), poison (Jormungand) or chibiko (Freya). That is why it is commonly advised against choosing Carlie or Kevin as the main hero.
Koren may be made a joke by using a gimmick, note Using Matango Oil or Hawk's magic (as Wanderer) Counter Magic will render 90% of his spells useless. but chances are you won't know it and will be bombarded by several magic spells with varying degrees of power cast from a very swift magician that uses Flash Step to get away from you all the time and can take inordinate amounts of punishment.
All of the six exclusive dungeons (Glass Desert and Dragon's Hole, Cave of Darkness and Dark Castle, Jungle of Illusion and Mirage Palace) are very long, have very little recovery points and chucks Demonic Spiders every now and then on you, not to mention the Boss Rush inside of each.
The Untwist: The Darkshine Knight is Duran's father. This is so obvious that he even calls Duran out for being too much of an idiot to notice it