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.
Game Breaker: Magic spamming in Seiken Densetsu 3. Also, the Kevin bug allows Kevin to shoot to absurd levels of strength if he transforms into a beastman at exactly the right moment.
While it takes longer, Magic spamming (particularly once you get Luna) is similarly game breaking in Secret of Mana. Even more so than Seiken Densetsu 3, considering the fact that the spell animations freeze the enemy in place, so casting with the right rhythm can allow the Sprite to kill any enemy before they can move.
Secret of Mana has a damage cap of 999. By the time you can actually reach that with spells, most bosses will have 3000+ HP, but then again, only two bosses in the entire game have over 5000HP. Also if you leveled up spells to "Level 9" (8:99), if you invoke a Level 9 animation, you effectively can't spam anymore.
Killing a boss in 4-6 hits is pretty dang game breaking. The level 9 animations slow down the magic spam but don't change the fact that the boss is being killed in 4-6 hits.
There's also the Sword Orb bug in Secret of Mana that you can exploit as soon as you get reliable means of transportation. If you exploit long enough, gives you a sword that can pretty much kill enemies in two hits, at most.
Having Blackpearl as your NPC assistant in Legend of Mana, since her support ability boosts your super meter to 100%. If you bother to learn Item Crafting, you can also deck yourself out with an arsenal of god-slaying that makes even the No Future Mode (ALL enemies lvl 99) a breeze.
Player Punch: Some parts of some games are so depressing it hurts the psyche:
Surprisingly Improved Sequel: Seiken Densetsu 2 (Secret of Mana) and 3 were both vast improvements over their predecessors. (Seiken Densetsu was first released in the US as the underwhelming Final Fantasy Adventure)
Legend of Mana also has the two Tropicallo fights where you can't attack it directly but can only take off a portion of its HP every time you defeat one of its tentacles. One casts magic at you nonstop unless you knock it off its perch, in which case it self destructs and takes a massive chunk of your HP, and the other attacks aggressively. Both continually respawn until the Tropicallo dies.
Seiken Densetsu 3 had the second fight against the Bill and Ben, two ninjas who will always counter any spell (and Limit Breaks count as spells) with their ninjitsu.
Vaporware - Seiken Densetsu: The Emergence of Excalibur was a Famicom Disk System game that started development in 1987. Its goals were too big for its britches, and the game collapsed under its own weight. A completely unrelated title named Gemma Knights was then renamed and released on the Game Boy as the series-starting game we're all familiar with; the creators thought the name Seiken Densetsu was too slick of a trademark to lose. More info can be found here.