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.
"Stray Bullet", from comic book story "Squirrely Burly" (issue #1).
"All Chalked Up," from Scholastic Book, same title.
"PowerProf.," from Scholastic Book "Powerpuff Professor."
"Substitute Creature," from Little Golden Book, same title.
"Neighbor Hood," from comic book story "Remote Controlled" (issue #7). The episode was originally penned for season 1 but fearing a lawsuit from the producers of Mister Rogers' Neighborhood, the outline was given to DC Comics for the comic story.
"Lying Around The House," indirectly from comic book story "Big Fish Story" (issue #21).
"Simian Says," indirectly from comic book story "See You Later, Narrator" (issue #46).
"Deja View" (comic issue #50) was intended as a season 5 episode but was shelved due to being overbudget (half of the ep was to be in CGI) and having a tight deadline. Like "Neighbor Hood"/"Remote Controlled," the story outline was given to DC and made into a comic.
In "Insect Inside" Blossom produces a giant jar to contain a mass of cockroaches. Lampshaded by the narrator who talks about Blossom's knowledge of where to get giant jars, and in a later episode where she pulls out a giant match, which she claims to have gotten from the same place.
During "HIM Diddle Riddle," the girls are tasked with taking down a giant monster without using their powers. Buttercup runs off and comes back in a helicopter with a gatling gun. Where did that come from, how did she get it, and how does she know how to pilot it?
Badass Decay: The first episode Him was introduced, he was presented as a hellish almighty powerful being so fearsome we can't even say his name, and was pretty solid Nightmare Fuel. By the last time we see him in the show he turned into just as much of a feeble joke as any other villain.
Though somewhat justified as Him draws power from evil, the more good around him the weaker he is.
And we've seen what would happen if he won as well, and it's notpretty. He may not be as deadly when last seen, but he's no doubt still dangerous to be taken lightly.
Big Lipped Alligator Moment: At the start of the episode "Catastrophe", the girls are shown at a ceremony where they are rewarded with a bronze statue and "Powerpuff Day". The ceremony is soon interrupted by a monster searching for his cat, who the girls leave to deal with. The ceremony is never mentioned again throughout the episode. .
Broken Base: The 2013 re-designs of the girls have solicited reactions raging from "awww how cute!" to "OH GOD KILL IT WITH FIRE!".
Complete Monster: One-shot villain Professor DickHardly. Introduced as the sleazy college roommate of Professor Utonium, Dick quickly sees the potential of the Powerpuff Girls as a way to get rich quick. Getting the girls to supply him with Chemical X, Dick makes his own knock-offs of the girls and starts a business selling these copies as superheroes. Due to Dick's greed, however, these knock-offs have been created with minimum materials and Chemical X, meaning that, even though they are aware, they are mentally stunted and physically deformed. When the effort of superheroing causes the knock-offs to fall apart, Dick's happy because it means he gets to sell even more copies. At one point Dick notices one of his knock-offs is a perfect Buttercup copy, his response is to order the girl melted down for her "excessive" Chemical X. The episode's climax has Dick capturing the real Powerpuff Girls and killing them slowly by draining them of their Chemical X. When Utonium offers to be a slave, making Chemical X for Dick for the rest of his life, if Dick will let the girls live, Dick only laughs and says he'll kill the girls and keep Utonium as a slave. Greed incarnate, Dick Hardley was the only villain on the show to be played completely seriously, with no humorous quirks to detract from his viciousness.
The children's song about Ms. Keane from "Substitute Creature".
La La Love, La La Love makes the world go 'rounddddd.
Ensemble Darkhorse: The Rowdyruff Boys were intended to be one shot villains, but they garnered such huge fan support with tons of fan art to even a website built around them (which is unfortunately now disabled, the link is to a archive of the site) that the writers eventually caved and brought them back, redesigned and having more depth then just being evil counterparts to the girls.
Bunny, the fourth Powerpuff Girl that Blossom, Bubbles, and Buttercup made, has some love from the fan-base, probably due to her episode being an absoluteTear Jerker. She's even mentioned in Bleedman's Powerpuff Girls Doujinshi.
Family-Unfriendly Aesop: In a society where children are told to cooperate, we have the episode "Monstra-City". An episode that shows the complications of immigration/integration. In the end the only thing they learned was that not everyone is able to live together.
Another episode seems to teach that if we respect our elders, or allow them to continue taking part in society, they'll just get themselves hurt.
Outside of Townsville, there's an agricultural disctrict called Farmville.
Judging by its color scheme, Him's demon piņata in "Birthday Bash" might possibly have been a sour.
Ho Yay: In the episode called "The City of Clipsville," Professor Utonium is about to marry Ms. Bellum. But then when he takes off her veil to see her face, it turns out to be Mojo Jojo who reveals that he has always loved the professor. This is also a serious example of Getting Crap Past the Radar.
Jerkass Woobie: Buttercup full-stop, if you think about it long enough. First of all, the professor had no good reason officially to name her Buttercup other than that it starts with "B". Second, she has no unique power (and tongue-rolling doesn't count). Finally, nobody really pays her any attention, and when they do, it's usually when she's in trouble. Even some fans never seemed to care much, instead opting to exploit her misery and attitude for kicks and giggles.
Jumping the Shark: One episode features a character named Rainbow the Clown who is hit by a truck full of bleach. It removes the color from his design and he becomes a villain called Mr. Mime. He then terrorizes the town. He's defeated by a cheery-upbeat song the Powerpuff Girls play, which restores his color and his previous nice demeanor. He thanks the Powerpuff Girls for saving him from his dark side... and then they beat him up anyway and toss him in jail. Even the narrator supports this. It's a very harsh and sudden conclusion since it really seemed like the villain was only acting as a villain because of being poisoned and not because he was a truly bad guy. Especially that this happened after the Powerpuff Girls saved the town by performing a song called 'Love Makes the World Go Round', it brought about severe Mood Whiplash. In many viewers eyes, this is when the series jumped the shark. ("They beat up the clown," was voted highest on when they jumped the shark on the old Jump the Shark website.)
Love to Hate: Him. He manages to be the most popular villain in the series to be incredibly frightening and efficient, especially in the earlier seasons.
Mojo Jojo as well.
Magnificent Bastard: Him, mainly in his earlier appearances. Sometimes Mojo Jojo, particularly in the movie.
From "Cover Up," a floored Buttercup's pathetic "Nooo" when a rather diminutive monster marches toward her. She just let herself get beaten up because she hadn't rubbed her good-luck blanket, but when taken out of context, this clip has some rather Unfortunate Implications. Needless to say, without context, Poopers had a field day remixing this clip.
"Eat your pea, Professor!"
Misaimed Fandom: In the Clip Show spoofing episode, one of the "flashbacks" was of the Powerpuff Girls being bimboish teenagers who have given up crime fighting to hang out at the mall and flirt with the also teenaged Rowdyruff Boys. The whole sequence is rumored to have been a parody of extremely bad PPG fanfiction. A great deal of fans completelymissed the point however, and the sequence ironically ended up inspiring even more fanfiction with similar plots.
Dick Hardley murdering a perfect Buttercup clone for her Chemical X. And later on, tries to kill the real Girls for more Chemical X.
Mojo arguably crossed it in the movie by enslaving Townsville with super monkeys, destroying half the town, and betraying the girls trust in the process. Since it was his first evil world domination plan, he apparently couldn't cross the line any further in the TV series. See Villain Decay. There is also a Fridge Horror as it is believed that in the same movie is out with a mass murder.
Also, once the Rowdyruff Boys started throwing vehicles full of innocent civilians at the powerpuff girls, that's when the girls decided it was time to stop trying to fight fair against them. (For contrast, the tactic the girls used in response was to look pretty and kiss said boys to overwhelm them!)
In-universe example: in Twas the Fight Before Christmas, Princess switches the nice and naughty lists to make it look like she's the only nice kid in the world. As soon as Santa finds out about this and actually sees how naughty Princess is due to her rubbing her demands on wanting to be a Powerpuff Girl in his face, he has no choice but to induct her onto the Permanent Naughty Plaque.
Princess making crime legal in Townsville in "Bought and Scold", solely to spite the Powerpuff Girls. From the same episode, the Mayor selling the town to Daddy Morbucks for "a room full of Turkish delight", allowing Princess to do the former.
One Episode Wonder: Dick Hardly. Indeed, while he came late in the series' lifespan, his episode is considered the best written within the Seasonal Rot and many fans even put him above Him as their favorite villain.
Paranoia Fuel: The episode "Supper Villain" hammers in that your average, everyday neighbor with an average, everyday family could actually be a sociopathic supervillian wannabe without anyone knowing it.
Periphery Demographic: At the peak of popularity, most of the show's fans were boys... not that every guy would admit to watching it in public.
Nowadays it seems fine to admit you watched this show. It was intended for both boys and girls though.
Poor Man's Substitute: Craig McCracken originally wanted Jack Black to voice the Gnome in "See Me, Feel Me, Gnomey" but by the time they got to production he was too busy and expensive, so they instead got Jess Harnell doing a Jack Black-like voice.
Special Effect Failure: There are some points in the series where you can clearly tell that characters have been chroma-keyed into the scene.
Villain Decay: If we look at things chronologically from the movie to the TV show, this happened to Mojo Jojo. He actually succeeded in taking over and destroying much of Townsville in the movie but is always failing in the show. He did, however, have the girls' help in the movie. They weren't so easily tricked afterwards.
More or less happened to a few other villains as well in The Movie. Before the Powerpuff Girls were around, the Gangreen Gang were a very frightening street gang. In the show, they often needed the help of someone else to even be considered a threat.
Villain Sue: Done on purpose with the Alien Force from "Forced Kin"... until the end.
All three Girls fall under this in "Sweet 'N Sour" where the Fluffy Bunch is robbing Townsville blind due to their blatant cuteness. It's hard not to wanna hug all three girls when the whole town turns on them and denounces them as animal haters.
What with the Adult Fear he goes through several times, it's hard not to feel bad for Professor Utonium, especially if one is a parent themselves.