Bottomless Magazines: If the player drops below a certain amount of ammunition (100 bullets) for Jim's default blaster, it will slowly replenish itself until it hits that number again once Jim stops firing. Which is good, since running out would spell disaster when dealing with Peter Puppy (who stops and ducks when he's shot at) or Evil Queen Slug-For-A-Butt (who just takes a lot of hits).
Bottomless Pits: Earthworm Jim: Menace 2 the Galaxy has one in the laboratory level. The implementation is egregious because a powerup on that level lets you fly up the same pit, and it doesn't trigger if you're on the other side of a one-way-wall on the side of the pit. Flying down said pit stops you against an invisible floor, has the floors below the pit visible, and is lethal until you exit the pit. To properly go down, find the non-bottomless pit on the same floor.
Easy-Mode Mockery: In talkie versions, instead of the ending you get a lecture about worms from Jim himself. You get the full ending on normal difficulty and a very uplifting speech if you finish on hard.
"For Pete's Sake", although the puppy you're escorting ALSO happens to be the biggest threat of the level. Several levels in the sequel task Jim to use a giant marshmallow to save Petey's children from being thrown out the window. It's roughly 357% less aggravating than the first game's Petey level.
Earthworm Jim 2 also contains "The Flyin' King", a level in Isometric Projection where Jim flies his handy Pocket Rocket through the hazardous skies to the boss. In order to beat the level, you have to gently bump a fragile and highly explosive balloon to the very end. If it ruptures before meeting the boss, you have to go back to the beginning to try again.
Funny Background Event: In the higher-end versions of the first game, the cow can be seen periodically going by in the background in later levels.
Gainax Ending \ Tomato Surprise: Done for hilarious effect in the second game: "And so, having defeated the nefarious COW Psy-crow, our hero, the COW Earthworm Jim, wins back the heart of the lovely COW Princess What's-Her-Name."
Gasshole: The boss of New Junk City arguably; it's not easy to be sure whether he's belching out or throwing up when he hocks dead fish at you. Given the artwork from the manual depicts him with a beard-like smear of vomit down his chest, he's probably vomiting the fish at you.
Hitbox Dissonance: Throughout many levels, many walls and ledges...aren't. Leading sometimes to some frustratingly cheap deaths, but also used to hide secret paths. Especially obvious in the final level.
In Case of Boss Fight, Break Glass: Inverted. The game has a level where you have to carefully guide an underwater vehicle around. More cracks appear in the glass every time you hit a wall. Oh, and there's a time limit.
Insect Queen: From the game and its respective cartoon, there is Queen Pulsating Bloated Festering Sweaty Pus-Filled Malformed Slug-for-a-Butt, who's a queen termite with a very squicky self-explanatory name.
Juggling Loaded Guns: Two of his idle animations are to twirl his blaster on his finger, throw it in the air, catch it and holster it. The aversion is done successfully, with no harm done. In the second (straight) version he catches it wrong, and it blasts him in the face. (Unfortunately, his head does not asplode.) A third idle animation splits the difference — after Jim tosses the gun in the air, it lands on his head, but doesn't go off.
No Plans, No Prototype, No Backup: Professor Monkey-For-A-Head originally invented Jim's suit, so why doesn't he just make another one? The monkey ate the plans after the prototype suit (what Jim wears) was made; he's after Jim to get the prototype so he can make a new one via reverse engineering.
Papa Dog: The "Puppy Love" levels in the second game involve trying to save Peter Puppy's kids, using a giant marshmallow, when Psy-Crow tries to throw them out a window. Let 3 get killed, and Peter rips Jim apart. Why he doesn't rip Psy-Crow apart is left nebulous.
Poison Mushroom: The Bubble Gun in the second game, although not directly harmful, is intentionally useless and meant to inconvenience the player. Worse in the Genesis version, which didn't allow for weapon swapping. It actually distracts the alien things. If there're a few of them attacking you and you shoot, they just fly around the bubbles until you run out.
Parodied in the manual for the SNES version - it claimed that the X button "turns on the porch light of Mrs. Schultz in Germany. So quit pressing it!" So naturally, what did everyone who read the manual do? Press the button. And of course, it does nothing at all.
Done again in the manual for 2, where the D-Pad "withdraws all moneys from your bank account and transfers them to Shiny Entertainment. It also makes Jim move."
The manual of the Genesis version of 2 says that the B-button "orders a large pepperoni pizza" in "The Flyin' King". Again, it does nothing.
Sequel Difficulty Drop: Compared to the first game, Earthworm Jim 2 has a lot fewer instant death traps (generally just bottomless pits, and even those are rare in 2), easier bosses, and generally less frustrating levels.
"What The Heck?" starts with a snippet from Mussorgsky's "Night on the Bald Mountain", then, following a Record Needle Scratch, switches to elevator music backed by screams of pain.
Andy Asteroids is a fast-paced race through an asteroid field set to banjo music.
Stealth Pun: Quite a lot. For example, one enemy in "What the Heck?" is a snowman, a reference to the phrase "a snowball's chance in hell".
Straw Scientist: Doug Tennapel, a self-professed Creationist (believer in Intelligent Design), has said that the Professor Monkey-For-A-Head character was created as a dig at some of his Darwinist teachers.
Tube Travel: The second game had this in the ISO 9000 level, though it looked painful (the entrance was a grinder).
Unexpected Gameplay Change: 2 has so much of it that... Let's say, after swimming in a salamander suit, taking part in a quiz show, bouncing puppies, bouncing explosive balloons, flying on a bloated head and carrying hamster cages around such unexpected gameplay changes are generally to be expected, at least since level four. That's while also making much of your collectible ammunition useless most of the time. Then the game throws you a ball by making Level Ate play like a more-or-less linear level with all your guns intact, and with the hot kitchen stoves being its only gimmick. To top it, even the pizza boss fight is done in a traditional "shoot him till he drops" fashion. Now, after all the adventures you've had before, this is quite unexpected.
That's right: EWJ just subverted a subversion trope.
Visual Pun: The homing missiles in the second game are shaped like houses.