In the episode "Not So Awesome Blossom", Blossom has run away, and Mojo Jojo has kidnapped The Professor and forces him to call the girls' hotline and read a note. Mojo's speaking/writing style + the Professor's monotone make the scene hilarious in a way that has to be heard to be understood.
Professor Utonium: Bubbles, Buttercup, or whichever of the two remaining Powerpuff Girls has answered the hotline, listen closely. Pay attention. Concentrate intently on the words coming from my mouth. I, The Professor, am being held prisoner. I am being kept against my will in a location not of my choosing. If you desire my safe return, you must come immediately to the lair of Mojo Jojo. Together. Not alone. Independently is not an option...
Buttercup: I think we're supposed to go to Mojo's and save the Professor.
Bubbles calls the hotline pretending to be the Mayor. The real Mayor picks up.
Mayor: What's that Mayor? A giant alligator is destroying Townsville! I'm on it. * Jumps out the window. Ms. Bellum comes up to him* Mayor: ...I... fell in the mud.
What really sells the Mayor's "I fell in the mud" line is the way he says it. Rather than sounding upset, it's a rather calm way that makes it seem like it's something he's regularly done before, which if anything, makes it even funnier.
When Mojo Jojo is babysitting the girls, he tells them a bedtime story which is a completely wrong account of Napoleon Bonaparte's conquests. The girls correct him with a detailed description of the later Napoleonic Wars, all while hitting him with pillows.
I always crack up at the game's message: "You just killed your own fairy."
The episode "Supper Villain"
"You'll never guess what's for breakfast... pan-cakes!" "This family stinks."
"Eat your pea, Professor!" The Professor proceeds to chew on a single pea for a minute. "SWALLOW IT!"
"Who wants dessert?" "I DO!" "AW, FOR CRYIN' OUT LOUD, MARIANNE!"
"DOES ANYBODY WANNA PLAY JACKS AFTER DINNER?"
"TAKE THIS, KIN OF EVIL!"
"We haven't kissed like that since 1980!"
In the sequel to this one, when the entire Smith family becomes supervillains, they give their reasons for wanting to turn evil. Bud (the son's) reason? "You know what? I hate everything!"
How much better the world was under Mojo Jojo's rule in "The Powerpuff Girls Rule!"
That episode was full of hilarious moments, with highlights like this:
The Mayor: I lost it! I lost the key! AHHHHHH!
Prof. Utonium: AHHHHHH!
The Narrator: AHHHHHH!
Buttercup: (Being shown as the dystopian ruler Big Butter) There's only one way to rule the world! Just tell everybody what to do and when to do it! And if any of 'em got a problem with it, they can take it up with Punchy McGee and Fisty O'Flannigan!
Compare that with Bubble's own idea to rule the world:
After Mojo Bubbles has been going on and on for awhile.
Mojo Jojo: Oh, SHUT UP! *conks her on the head again* That's all just well enough, because in reality there is only room enough in this world for one Mojo Jojo. One shall be the number of Mojo Jojos in the world and the number of Mojo Jojos in the world shall be one! Two Mojo Jojos is too many,and three is right out! So the only Mojo Jojo there is room for in the world shall be me! And being the only Mojo Jojo in the world, I will rule the world, in which there is only one MOJO JOJO!
Then, as Mojo (now a sumo wrester) is at a great advantage against the girls (now a cobra, caterpillar, and wiener dog), against all probability, the girls are transformed into a fisherman, sushi chef, and eskimo, while Mojo becomes a fish.
"Professor, your hand doesn't work!"
In "Him Diddle Riddle" the girls have to solve various riddles by a certain amount of time, or else the Professor will pay. The girls lose eventually and the Professor ends up, well, having to pay... for the pancakes Him made at a diner. The pancakes would've been free if the girls had solved the riddles in time.
The Powerpuffs have to take the SATs, needing to get over 100 total to pass the test. Buttercup gets a 25. Blossom gets a 12. Bubbles, whose answer sheet was filled out to form a daisy, got over a thousand.
Him: (dumbfounded) Well, I'll be darned.
The Narrator's reaction to the reveal at the end.
Narrator: And so... um... yeah...
Then there's the final riddle, which is answered by The Mayor of all people, who effortlessy decodes the meaning of 'boiling and freezing' as coordinates, figures out what area they lead to, then throws in, "...Or maybe there's an ice cream truck on fire."
In the episode "Mime for a Change".
Bubbles: (on why we need color) Not to mention all the safety reasons!
(Car parks in front of fire hydrant. Bubbles picks up car.)
Bubbles: You can't park in front of a fire hydrant! (Throws the car)
Driver: I didn't knoooooooow!
Upon confronting Mr. Mime.
Blossom: So, you like to make things black and white, huh?!
Buttercup: Well, how would you like to be black and blue?!
The entire "Curses" episode. Starting with Bubbles saying "Stupid [censored] crayon!"
This exchange takes the cake:
Blossom: It's obviously an adjective that can be used for good and bad words. There's great, there's super great, and then there's [cat hissing] great!
Princess talking on the phone in "Boy Toys".
Princess: Now look, monkey butt, it's real simple! Take your cheap, good-for-nothing, lazy soy latte, honey, and leap out a high window 'cause you're breathing my air, and you are fired! Ugh! *hangs up* Man, my mom can be such a pain in the butt.
In "Too Pooped to Puff", The Professor can't reach the remote. The girls get fed up with his laziness and leave, except for Bubbles. Bubbles smiles and picks up the remote, then promptly drops it on the floor and exits.
The townspeople trying to defeat the monster..."If we force the monster to take a bath, his toast will get soggy!"
In "Meet the Beat Alls" Mojo and HIM are having a Eviler than Thou argument which Princess interrupts insisting that she'll be the one to beat the girls because she has the greatest power of all: cold hard cash.
Mojo: She has a point there. Him: (effeminate voice) Yes, she does. [long beat] Mojo: But, still. Him: Yes. *resume fight*
Boomer: You girls are gonna eat your words, spit 'em out, and eat 'em again! Blossom: That doesn't even make sense! Boomer: I know you are, but what am I?!
From "The Powerpuff Girls Rule!"
Narrator: All of the villains and all of the bratty ones and all the fuzzy ones and all the icky ones and all the sticky ones and all the scary ones and all the villains are- Mojo: One of us is not here!
The competition the villains have as they literally tear up the city in search for the key to world domination. It become so ridiculous that the girls just have to stand there gawking at how stupid they act while they fight each other in a Big Ball of Violence. And then comes the go-kart-like race they all have to the Mayor's office.
Mojo Jojo's reaction when the girls beat him in getting the key in the Mayor's office.
Professor Utonium has shrunken down the girls so they can fight off an invasion of Nanobots more easily. However, the nanobots all fuse together to form a robot a few inches tall, an impossible foe for the girls to fight off, because of the sheer size advantage. Cue The very normal-sized Professor just stomping the robot once.
From "Who, What, When, Where, Why... Who Cares?", the documentary made for the show's 10th anniversary, when explaining Craig McCracken's background:
Narrator: The city of Los Angeles! With the passing of Craig's father his mother decided to move on to greener, more earthquake-prone pastures."
And when discussing McCracken meeting his co-worker and future wife Lauren Faust:
Narrator: He had to be sure he was thinking with his mind and not just his, uh... Mayor: Pickle! Narrator: Right, Mayor!
And McCracken's final line of the feature to the narrator: "Tom, you're out of a job."
Season 1, Episode 2: "Powerpuff Bluff". About a trio of criminals who impersonate the Powerpuff Girls.
Blossom: (the crooks are threatening to break a priceless porcelain poodle and the girls bust in) Put down the priceless porcelain poodle, you punks! Lead Crook: P-p-p-Powerpuffs! Blossom: Precisely!
Halfway through the episode, a pickup line and the (not-so-sexual) Double Entendre that follows it.
Bubba: Hey, Sweet Cheeks! What's your sign?
Sara Bellum: Stop.
The Imagine Spots in "Substitute Creature". Especially when combined with the outrageously melodramatic dialog.
Elmer Sglue:No, Mr. Green! I don't want to be spun!
Everything about "Meet the Beat-alls" episode. The non-stop references were all too much for me to take. And their plan to use a monkey Yoko Ono to break up the group was sheer brilliance.
"Powerprof." The whole fight scene where the Professor embarrasses the girls with horrible one-liners and pet names is pretty funny, but what really puts it over the top (and puts Bubbles' face into a paper bag for the rest of the scene) is the Professor casually mentioning to bystanders:
Professor: My little Bubbles. You'd never guess that only a few months ago she had a bed-wetting problem!
The entirety of the episode "Jewel of the Aisle". "Ridiculous, Lucky Captain Rabbit King! Lucky Captain Rabbit King Nuggets are for the youth!"
Mojo: (Bloodshot eyes and grinning) I know who took my plans...It was you! (Points at bluebird) Well then...It was you! (Points at phone) It was all of you!
From "Bubblevicious", the source of a massive traffic jam is revealed to be a dog: "Well I may be able to talk but I sure as heck can't drive!" Followed immediately by:
Dog: Bubbles.. have mercy..
Bubbles:Mercy is for the weak!! [WHAM]
In the same episode, when Bubbles is in the training simulator, the Professor turns the Danger Level down to 2. She winds up in a normal room, devoid of any monsters. Confused, she looks around, the door opens, and...
Robot: Boo. I'm gonna get you. Boo. I'm gonna get you. Boo. I'm gonna get you. Boo.
from Live and Let Dynamo, the girls are trying to figure out who could possibly piloting their giant robot.
Blossum: Whoever is in there must be the most ruthless, sadistic, lover of carnage we know.
(Mike hands those over too. He then offers his gun)
Da Chief: Uh, no, no, you can keep that. Little souvenir for you. That donut's lookin' pretty good, though. (Gets Mike's donut) Awww, yeah.
When each of the girls gets knocked into the Mayor's window during their first fight with the Rowdyruff Boys, he just casually says hello to each of them all while going on about a pretzel-related holiday he's planning on declaring in the town.
Mojo Jojo singing "Everybody Wants to Rule the World" by Tears for Fears in "Powerpuff Girls Rule".
There's a lot in "Telephonies" - including Him's terrifying exercise routine - but the best is the Professor, who "wins a million dollars" in a prank call and is told to stay on hold...and does...for the entire episode...without moving at all.
If not the entire Affectionate Parody of Rocky and Bullwinkle in "I See a Funny Cartoon in your Future", then at least the moment when the absolute worst pun of the bunch ("We're not just dealing with a petty criminal - we're dealing with a tarot-ist!") is followed by a long Beat to really let it sink in.
While the backlash on the girls due to their doubts on the Fluffy Bunch in "Sweet 'N Sour" is rather heartbreaking, this scene is admittedly funny:
Also counts as a Moment Of Awesome, seeing how Bubbles is willing to stand up for herself and her sisters when the city starts hating them.
In "City of Clipsville," the flashback to the Professor and Ms. Bellum's wedding, especially the punchline:
Mojo Jojo (in a wedding dress): I have always loved you.
Princess decides to hatch up a plan to destroy the Powerpuff Girls with Mojo Jojo. She tells him this from the bottom of his mountain, shouting at the top of her voice in the middle of a crowded day.
Princess: You big buffoon!
Mojo: I am NOT a baboon!
The episode "Silent Treatment".
At the end of "Members Only", when the Girls prove themselves to the members of the AWSM by defeating Mascumax, the way the villain goes on as he amscrays in humiliation makes him sound like a bully who has gotten a heaping dose of his own medicine.