These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anti-Climax Boss: Bob the Goldfish — depending on the game and version, Jim does everything from simply tip his bowl over and leave him flopping on the ground to eating him.
It's also possible to kill Queen Slug-For-A-Butt in one hit with the whip. The HD version even encourages this!
The second act of every episode starts with a short sketch that has nothing whatsoever to do with the plot. After it plays out, the narrator will announce that it's time to get back to the story.
Ear Worm: Basically every musical piece in the game, which ranged from creepy Danny Elfman-like weirdness, to classical music, to funk/electronica/pop.
Fanon Discontinuity: Earthworm Jim 3D, Menace 2 the Galaxy and the GBA rereleases are often subject to this.
There are also some people who ignore Earthworm Jim HD, or at least the new features, due to said new features being made without the involvement of the original team.
High Octane Nightmare Fuel: The music for the Intestinal Distress and Big Bruty stages are creepy. Especially compared to the rest of the music in the game. And Queen-Slug-For-A-Butt's graphic explosion after you defeat her in the first game.
The background during the boss battle with Evil the Cat features a legion of creepy, malicious stone faces. In some versions of the game, however, there`s just a regular pitch black background.
Moment Of Awesome: For the TV series, the end of "The Egg Beater." After Jim fought them in separate battles throughout the episode, his usual enemies get together to eliminate him. That's seven (eight if you count the monkey) enemies, as well as a stressed-out, transformed Peter Puppy to worry about. In the ensuing battle royale, Jim either outsmarts or outright Curb Stomps them all before a more prolonged battle with the Queen that sees her beaten. And he keeps count of his victories in the process!
Nausea Fuel: From "Snot A Problem" to "Intestinal Distress," the series is notorious for grossing people out, primarily on purpose.
Porting Disaster: The first game was on many systems, but with the exception of the Sega CD and PC version, it got worse with each one! It lost a level on the SNES version, and you should expect what happened when they tried to port a game that pushed the Sega Genesis and Super Nintendo to the very limit onto the Game Gear and Game Boy. The GBA port of the first game wasn't all that bad, even adding the missing level from the SNES game. But EWJ 2 on the other hand was a disaster.
The recent "HD" remake for PS3/360 was pretty good; only one problem: They omitted the secret level "Who Turned Out the Lights?" for some unknown reason. So the problem continues to this day.
The SNES version also took a lot longer to actually start the levels, almost like it was loading them. The underwater stage was also missing its music, using New Junk City's theme instead.
PC port tends to be remembered fondly, but not many realize there are two ports of the first game, that are made by two teams: one is a Special Edition port for Windows 95, other is a DOS port that came in Whole Can O'Worms edition. And while first is pretty good, second is not. While graphics are good and music was taken from Sega CD version, the controls are so-so, collision detection is not that good either and they took out not one, but two levels (Intestinal Distress and Who Turned Out The Lights?). The same team made PC port of Earthworm Jim 2, which has identical features to their port of EWJ 1, but this time they took out only one level (Lorenzen's Soil). The saddest part is the version now available at GOG.com and Steam is the second one.
The Woobie: Peter Puppy. Seriously, watch his backstory episode and then watch Sidekicked right after it and just watch his woobiness factor skyrocket.