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.
Demonic Spiders: If you ever run into an invisible enemy, prepare for pain.
Game Breaker: One item, creatable from about the game's mid-point, is a backpack that heals your robot each turn. Get it, and max the bot's Defense, and losing becomes basically impossible.
Goddamn Bats: Mole enemies in the volcano level. They randomly hide in the ground, making them invulnerable for that turn, have a screen-wide earthquake attack that not only damages you but destroys capsules, and use a melee attack designed to hit your back.
That One Attack: Confusion. Any enemy that can use it can lock you in a near-endless cycle of uncontrolled movement unless you save against it, which even a fully-upgraded robot cannot do reliably.
That One Boss: Being an Enix game, the list of bosses that aren't in this category is smaller.
Meta Crab: A Wake-Up Call Boss, if anything. Long-range attacks don't work on him, even the easily spammable big-bang attack.
Mamurana: Not only does she do moderate damage, but she constantly splits into clones.
Big Eye: He hurts. A lot. If you wasted your Scrap 9 on something other than Shield 4, this is effectively a stopping point in the game until grinding overtakes his power.
Black Tank: Continues the trend that Big Eye started.
DeRose: The poster child for this trope. She has the most HP in the game aside from the final boss (About 5000), a confusing laser attack, a powerful nuke attack, and essentially an instant death melee attack. It's also impossible to do more than Scratch Damage unless Axe 3 is used with the triple hit combo, and all three have to hit. The fight is trying to hurt her faster than she can deplete your stock of Cures.