Eldritch Location: Technically, the whole game as you are on an alien planet. The levels progress with no rhyme or reason to them. The scenery often changes radically from happy to grotesque, not only the first level but several of the boss rooms are more macabre in nature than the levels.
Flash of Pain: Bosses briefly turn white when hit. As for the regular enemies, it depends on the enemy type to determine which color it turns into when hit.
Getting Crap Past the Radar: The "level start" and "game over" screens show skeletons waist-deep in a lake of blood. No idea how that slipped past Nintendo's censors.
Not to mention when the very first level transforms into a hellish landscape after you pass by the big tree. This effect was supposed to happen in every level in the original game.
And they slipped in the word "Hell", which wasn't allowed in the NES days. Ditto the word "die", spoken by the final boss.
The original Japanese prototype was actually much scarier from what screenshots from magazines reveal, so not everything got past the censors. For example, the huge amount of slime oozing from the monster's mouth in the title screen was originally supposed to be blood.
Now that we have a Japanese prototype, it was clear that they had many references that were caught by the American radar. Namely an Alien (along with eggs containing facehuggers), a Mogwai, and The Thing.
Our Monsters Are Weird: Most of the game's entertainment value comes from the sheer lunacy of the enemies it throws at you. Burning Japanese schoolboys! Angelic sticks of dynamite! Joseph Merrick, for crap's sake!
Temple of Doom: Level 4 is set in an Egyptian tomb, complete with scorpions, sculptures of Anubis, hieroglyphs, etc. What it doesn't have are the game's two Egyptian-themed bosses, who appear in other levels....
Tennis Boss: Most bosses shoot projectiles that you can knock back with Mark's bat. You do NOT want to face them as Bert.
Unwinnable by Mistake: One nasty and cruel example, depending on if you watch the key icon or not: Killing 2 bosses in Round 7 gives you a key, but killing the final one takes the key away, forcing you to restart the game.
Ventriloquism: The serpent dragon's speech bubble is pointing toward the right side of the screen, but it's on the left.
Zero-Effort Boss: One of the bosses on level one says, "SORRY, I'M DEAD." He does nothing at all and you can leave with the prize just a second later.
Another boss has two zombies requesting for you to watch them dance. If they finish their dance, you get the prize. If you hit them while they dance, they'll fall apart and then regenerate to start the dance again.