Rain, Rain, Go Away: "The Powerpuff Girls' Best Rainy Day Adventure Ever". Also the title of a story in issue #66 of the comic book.
"Rashomon"-Style: In one episode, the Mayor is kidnapped by Mojo Jojo and blindfolded. The girls save the Mayor and beat Mojo Jojo, but can't stop laughing after. The Mayor asks why. The girls each tell the story of how they saved the day today differently, accompanied by Art Shifts. What they neglect to mention? The Mayor was naked all along.
Reality Ensues: Everything related to the town of Citiesville, most notably the girls' destruction of the bridge leading in to town to stop some robbers. The bridge was both the only way for workers to commute to Citiesville and a historical landmark, costing over three million dollars. Reality Ensues, and hard.
Blossom: You know Buttercup, you may be clean but your attitude still stinks.
She's pretty good at giving these. One of her best examples is after the first time she defeats Princess.
Blossom: You're just a spoiled brat. And being a Powerpuff Girl isn't about getting your way, or having the best stuff, or being popular or powerful. It's about using your own unique abilities to help people and the world we all live in. And you, little girl, have done nothing worthy of the name "Powerpuff".
The Professor gives a big one to the Mayor on Toast Of The Town, calling him out on his childish behavior:
Professor Utonium: Wowie zowie indeed! Have you no shame? A grown man your age gallivanting around like a little child, not doing what you're told! "Mayor wanna this! Mayor wanna that!" You, Mr. Mayor, are nothing but a baby! A big, big, big baby!
The Zen master from "Makes Zen To Me" gives one to Mojo Jojo when he wants to take over as the master.
Master: You came seeking only violence. You were impatient. You would not look inside yourself. I could only guide you; the journey was yours to make. I did not fail you nor the teachings. You failed yourself. And another thing: You're not a monkey, you're a chimp. There's a difference.
Reunion Show: 2008's "Powerpuff Girls Rule", a PPG special made five years after the show ended, featuring nearly every main character within the series, as well as all the original voice actors.
Rhyming with Itself: In "See Me, Feel Me, Gnomey", this trope is rather egregious when the PPG join in Professor Utonium's "Freedom Beef" song, as they rhyme "peace" with itself rather forcefully, directly after rhyming "powers" with itself.
Rogues Gallery: Mojo Jojo, Fuzzy Lumpkins, The Gangreen Gang, Him, Princess Morbucks, Sedusa, The Rowdyruff Boys to a lesser extent and The Amoeba Boys if you consider irritation to be roguish. Mister Mime (the alternate personality of Rainbow the Clown) has also appeared in the background
Scantron Picture: Him once gives the girls such a test in a challenge, and although Blossom and Buttercup take the test seriously, they fail as a result. Bubbles passes, and it turns out she filled in the bubbles in the shape of a flower.
The comic book story "Steal A Meal" (Cartoon Network Block Party #26) has the girls doing a tearful Big "NO!" upon learning that after all the breakfast cereal in town had been stolen the only thing left was oatmeal.
Space Is Noisy: The few times the girls go into space, they can communicate with each other just fine.
Spear Counterpart: The Rowdyruff Boys, Brick (red color scheme), Boomer (blue color scheme), and Butch (dark green color scheme) to the Powerpuff Girls, Blossom (pink color scheme), Bubbles (cyan color scheme), and Buttercup (green color scheme).
The girls can fly faster than the speed of light. At top speed, they have been known to bend the time-space continuum and perform Time Travel, thus creating an Alternate Universe where there has been no Power Puff Girls to save the day for fifty years.
Gangreen Gang member Lil Arturo temporarily gains this ability in "Power Lunch".
One of the later criticisms of the series was that the show promoted animal cruelty because of their treatment of Mojo. Episode 57 ("Save Mojo") depicted a group of animal rights activists protecting Mojo from the girls despite their argument that Mojo is an evil animal and therefore others must be protected from him.
Two episodes featured the Smith family, one member of which was their angry teen son Bud. The first episode, Bud's entire appearance consisted of him yelling something typically teenagerish at his father, such as "I hate you!" and "No one understands me!" The second episode, which features the entire family as villains, provides every member of the family with a motivation for why they hate the Powerpuff Girls - and Bud's is "You know what? I hate everything!"
Also, the Gangreen Gang. Literally.
Teeth Flying: Bad guys' teeth go flying in the opening sequence; also, one episode is pretty much based on this trope - Buttercup learns the Tooth Fairy gives you money for teeth, and starts deliberately knocking villains' teeth out and collecting them to make a huge windfall.
Too Dumb to Live: The mayor. In one episode he jumped out a window because Bubbles told him to go save the day... while pretending to be him.
Took a Level in Badass: Bubbles in "Bubblevicious" to prove she's hardcore. She even subverted her apparent chickification when Mojo captured her and gave her the full blunt of his torture device before she broke out and beat him mercilessly all by herself. She only softens from her tough exterior when her sisters finally admit that she's hardcore, only to slide right back into it when Mojo tried to make a cheap shot at all three of them.
Twist Ending: The episode "HIM Diddle Riddle" revolves around the girls flying around town, trying to solve HIM's insidious riddles in a desperate attempt to save Professor Utonium, only to fail, and now HIM is going to make the professor PAY!... full price for breakfast. The ending is such a big wtf, that the narrator just stumbles, "And once again, the day is... um... yeah..." while the girls just float there staring blankly.
Unfortunate Implications: Touched upon In-Universe. In the "Members Only" episode, Major Glory talks the girls through several gender roles, asking who does various things ("Who goes to work?", "Who pays the bills?", etc) and receiving "Our Dad" as an answer each time. Then he gets to cooking and cleaning, getting the same answer. 5:12 - 5:45
Major Glory: So what does your mother do?
Girls: (in unison) We don't have a mother.
*cut to Major Glory looking over at Mucho Muchacho and Birdman, all three looking uncomfortable*
To drive it in further, Batman was earlier shown sitting next to Birdman, meaning he would've been just off-screen for this.
The Unintelligible: Grubber of the Gangreen Gang usually speaks only in raspberries. The rest of the gang members understand him just fine though. Subverted in one episode, where Grubber is shown to be quite eloquent when he straightens his posture. He's also an expert voice mimicker.
Unwilling Suspension: In "Equal Fights," as Femme Fatale falls to the ground, Buttercup grabs her foot and carries her off upside down.
"I See A Funny Cartoon In Your Future" has Madame Argentina tying up three voodoo dolls of the Powerpuffs and hanging them from a tree branch, causing the girls themselves to hang in midair over a cliff.
The splash page of comic book story "The Devil's Playground" (Block Party #43) has Him using his powers to booby-trap the kindergarten playground. Several kids are wrapped up in jungle vines from the jungle gym, and three monkeys appear on the monkey bars—the first holding a boy up by his hands, the second giving Mitch a wedgie, and the third using its tail to hang a girl upside down by one foot.
Up to Eleven: In "Bubblevicious" Bubbles takes the battle simulator and Mojo's laser up to eleven. The dial even shows considerable resistance, like it was never meant to go that high.
Villainous Breakdown: Mojo has these occasionally, most notably at the beginning of "The Rowdyruff Boys", when he starts howling and snarling like a real ape over his many defeats.
Mojo Jojo has a particularly huge one at the end of "Forced Kin" when he finally snaps after being repeatedly defeated by the alien force's Villain Sue trait of unrealistically predicting every attack. But the one thing the alien force didn't predict was Mojo going berserk and beating the crap out of it.
HIM also has these, normally after the girls defeat his plans with their sisterly love. He goes from his normal, creepy voice to screaming about how they didn't act like they were supposed to. He has an especially noteable one at the end of "Power Noia", when the girls have turned the tables on him and got him completely at their mercy, for the first time actually begging them to let him go.
Villainous Friendship: Mojo Jojo and HIM. The two often argue over who is the most evil, but at the end of the day, they'll get along.
Villains Out Shopping: Often. When the super villains aren't doing anything overtly villainous, they're treated like any other citizen of the town. Even by the girls themselves!
Very Special Episode: Even though it's not blantantly stated, "Mojo Jonesin" is obviously a drug episode.
Voice Changeling: Grubber uses this ability in the episode "Telephonies" to stir up trouble.
Walk Through The Camera: In the episode "Stray Bullet" in the scene where Mojo is walking very slowly with a confident look on his face.
Wanting Is Better Than Having: One episode had a collector of Powerpuff Girls' merchandise who freaks out and becomes a villain when his collection is complete: there's nothing left for him to collect except the girls themselves.
Waxing Lyrical: All over the place in "Meet the Beat-Alls", essentially a long string of Shout-Outs to The Beatles. Example; when Professor Utonium has an idea to defeat the combined forces of Mojo, Him, Princess Morebucks and Fuzzy Lumpkins, he asks, "Listen, do you want to know a secret?" Even the narrator gets into the act at the very end, declaring, "I don't really want to stop the show, but I thought you might like to know...that Once again the day is saved..."
Was Too Hard On Her: Bubbles asks this after the sisters scold Bunny for releasing criminals from jail...only for the criminals to show up and yell "Not as hard as we're gonna be on you!"
When Elders Attack: An old lady does this from the roof of an episode to a Godzilla-like monster, who promptly eats her.
Where the Hell Is Springfield?: Possibly subverted, if the Professor's directions to his college roommate were correct, Townsville fall somewhere in or near Pasadena, CA. Don't mind that there actually exists a City of Townsville.
According to Mayor, the town is at latitude 32 degrees north by longitude 212 degrees west. The aforementioned Pasadena is at latitude 34 degrees north, but longitude 212 degrees doesn't exist (it stops at 180).
Who Would Want to Watch Us?: One episode featured a con-artist "director" allegedly making a movie about the girls. The initial broadcast of this episode was suspiciously close to the release of the actual movie.
Window Pain: Not only do things get thrown through windows, but driven. And the girls occasionally fly through them!
Yoko Oh No: invoked The Powerpuff Girls' plan to break up The Beat-alls. "Moko Jono" is the Yoko to Mojo Jojo's John Lennon.
What makes this not necessarily a YMMV, unlike most examples, is that she's literally the Yoko. The entire episode parodies the history and the songs of the Beatles; it's only obvious that the one who divides the Bad Four is a playoff of Yoko Ono.
This may be a subversion today as Paul McCartney had gone on record recently saying that Yoko was not the reason the Beatles split up.