- If you're playing any of the official translations, the first time you see Balrog, he crashes through the wall and yells "Oh Yeaaah!!"◊
- If you scale The Doctor's tower and go past the weapon stockpile at the top, you'll find a sign that says "THAT'S ALL FOLKS!"
- In the official translation, this was replaced with "End of the road!"
- On the Plantation in one of the jail cells you'll find a Mimiga that says "Doctor Dumb can go screw himself!"
- In the official translation, this was replaced with "The Doctor can eat it!"
- The Credits sequence, specifically Momorin and others trying to change Sue and Itoh back. Baleful Polymorph via Sneeze of Doom!
- One of the achievements for the Steam version involves being killed... by Toroko, weakly flailing a stick.
- When Mr. Traveller and Curly reach the end of the Labyrinth, they find a huge rock you can't both open. Balrog shows up and makes his usual threats while an oblivious Curly asks that he help move the rock. He starts doing so... then suddenly knocks both of them back and shouts "ARE YOU EVEN LISTENING TO ME?"
- What makes this even better is that, after Curly asks for help, Balrog's theme just stops, as Balrog blinks a few times as if to say "Did she just...?"
- The first time you meet Balrog, he argues with Misery about taking credit for catching Sue. The next time you see him, he seems not to remember that at all when he says Misery was punished for it.
- The cinematic in the Egg Corridor where Sue attempts to fight Igor. She uses the fact that she can beat up her wimpy brother as a threat. Igor proceeds to start punching her, and she attempts to surrender at every punch. The squeak sounds made and her expressions/lines are what make the scene funny.
- Talk to the Mimigas during the battle against the Doctor, one of them will snark about the "interesting priorities you've got".
- One of the many Easter Eggs has you finding Curly's Underwear. Make of that what you will.
- Another Easter Egg involves you sleeping in Chaco's bed, and when you wake up you find Chaco sleeping in the bed with you. If you check your inventory, you can now find "Chaco's Lipstick".
- The first fight against Balrog is an Optional Boss. He asks if you want to fight. Say no and he'll politely leave.
- The reveal that the fearsome Monster X is a random giant cat, humorously foreshadowed by the cat-paw prints on the tank and the fish-head protagonist-seeking missiles.
- The Nemesis weapon. At Level 1, it fires reasonably powerful projectiles. At Level 2, it shoots...weaker shots. At Level 3, it shoots rubber ducks that do Scratch Damage. The kicker is that leveling up takes only one EXP.
- Santa has instant death spikes in his house for whatever reason, with a sign reading "Watch out! Instant death trap to your left. One touch means instant death!"
Funny / Cave Story