The first one was so awesome, it made it into I Wanna Be the Guy as the theme for the Final Tower of the Guy, continuing on for The Guy's first form!
Breather Boss: King Bee is considered MUCH easier than the previous two bosses and the following boss.
Complete Monster: Lucifer, the Big Bad of the PC-98 game, is far more evil than the villains of the SNES successor. Having tricked numerous civilizations in the solar system into destroying themselves, most recently on the moon, Lucifer now intends to do the same on Earth. She starts at the beginning of life by driving numerous fish insane and destroying the peaceful nature of a small fish village. Later, her attempts to Kill 'em All become more direct, culminating in singlehandedly causing the extinction of the dinosaurs before gloating to Gaia, the embodiment of the Earth, that she killed everyone. In the last main chapter, after learning that there's still life around, she provokes a war between two colonies of Lunarian survivors by making one of them, Atlantis, obsessed with destroying everything, starting with the rival colony of Mu. This results in the destruction of both colonies. After her defeat and the establishment of human civilization, she gathers power for one last attempt to kill everyone in modern times, resulting in the destruction of the Moon and, consequently, the death of Gaia's sister, before Lucifer is finally killed for good.
Demonic Spiders: Many enemies can be this, but the Tyrannosaurus and Allosaurus are the worst of the bunch, being able to cause massive damage very quickly, and also being nearly unbeatable if you're not tall enough.
Developers' Foresight: Defeating the King Bee causes the giant bees to stop spawning in the two areas where they appeared.
Game-Breaker: Boss fights become much easier once the player discovers that undergoing an evolutionary change also has the beneficial side-effect of also healing all your health. Just stock up on EVO points prior to the battle, and when you're getting your ass kicked, just go to your evolution menu and make one small change (like adding a horn), and you'll be back in business.
Also, Cro-Maine. After he tells you his story (namely, how he was bullied by the Monkey-Humans), he suddenly changes from a calm demeanor◊ to being extremely pissed off◊. This forum even mentions that he has emotional issues. If so... just how severely the Monkey-Humans abused him if he is so violent and moody?
Goddamned Bats: Trilobites in the Fish Age chapter, most flying enemies if you're not a bird, and the monkeys and dino-people in the final chapter.
It Was His Sled: The Final Boss is a monstrous cell with an awesome battle theme. Thanks to I Wanna Be The Guy, this song is the first thing related to the game some newer players learn.
Moral Event Horizon: In the original, Lucifer firmly crosses it when she has the Great King of Terror wipe out the dinosaurs and proceeds to gloat how she killed everyone.
Most Wonderful Sound: Bolbox makes a very disturbing sound when hit, but when you beat him, he keeps doing it, and it sounds much better as he dissolves to nothing.
Nightmare Fuel: Bolbox can be this sometimes. The level with the cockroaches borders on it as well. As for the Queen Bee's face... ouch.
Older Than They Think: The SNES game itself is HEAVILY based on a much older game by Enix called 46 Okunen Monogatari: The Shinka Ron ("4.6 Billion Year Story: The Theory of Evolution"), released only in Japan in 1990 on a very obscure home computer called the PC-9801.
Signature Scene: The final battle with Bolbox. Mainly because of how bizarre the entire scenario is, the awesome music, and the brutal difficulty. In fact, thanks to I Wanna Be the Guy, this might be the first part of the game one learns about.
Mt. Brave is partly this trope and Brutal Bonus Level (it's optional). Birds pick you up and force you to start over. And the reward you get... is becoming a new class of evolutions, forcing you to start over. Unless you figure out how the Cloud Maze and River of Asteroids work, which give you the REAL reward: The Dragon and Gargoyle forms, along with a ton of Evo Points.
The Woobie: Yeti Avenger and Cro-Maine. The former one is the descendant of the Yetis you killed (humiliating the Yeti race in the process), while the latter one was a victim of abuse and bullying by his own kinsmen, the Monkey-Humans, because he had less hair and was smarter than the rest.