Robotrek/YMMV

Breather Boss: Bug Bug, both times.
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.
Hilarious in Hindsight: A RPG game about a lone child protagonist going to save the world with a battle system about having said kid throw a red and white ball on the battlefield which explodes to free a being that the player then has fight for them. Are we talking about Robotrek or Pokémon? Made all the more amusing due to several Pokemon like Polygon that have a mechanized look and/or artificial origin.
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 that aren't these 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 takes over.
- 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.