Seriously, any moment involving Mxyzptlk is a Crowning Moment of Funny. For example, we have his FIRST meeting with Superman...
Clark: A game has rules. Your stunts are just random idiocy. Mxy: Okay, I'll give you a rule, you make me say, spell or otherwise reveal my name backwards, and I'll split until our dimensions come into alignment again in about, oh, three months, give or take. Clark: I can't even say your name forward, how am I supposed to say it backwards? Mxy No, dope! You don't have to say it backwards! You have to get me to say it!! Clark: Say what? Mxy: KLTPZYXM!! Gosh you're thick! Now, for the last time- Aw nuts *poof*
Fast forward to three months later...
Mxy: Hi guy! Your three months are up. And this time, you're not gonna cheat me out of my fun! Clark: Oh, it's you again, Mr. Kltpzyxm. Mxy:Not "Kltpzyxm!" Mxyzptlk! Now, the first thing I'm gonna do- Aw, nuts. *poof*
He builds Powered Armor (complete with pants zipper!), goes to fight Superman, and doesn't last three seconds. Whatever happened is a Noodle Incident, but his reaction after the defeat just sells it.
His counterpart, Gsptlsnz, sells it perfectly the moment he leaves.
Lois: Don't you look happy. What's wrong? Bad news? Clark: [depressed] You could say that. I'm expecting a "visitor" from "out of town." Lois: The guy's kind of a pest, is he? Clark: The worst. Lois: I hear ya. Every time my sister visits, she moves right on in and stays and stays and... [a penguin suddenly waddles by] Lois: Was that a penguin? Clark: [starts tapping his pencil, annoyed beyond description] I'm afraid so. [Lois turns into a horse and neighs] Clark: Here we go.
The fact that in the fifth dimension, months apparently have names like George, Relish, and Pants.
When Superman starts pretending to give up as part of a ploy to get him to change the rules, Mxyzptlk threatens to tell everyone his secret identity, to which Superman just calmly replies that he'll find another disguise. What sells this one is the smug way Mxy holds up a newspaper reading "Superman is Clark Kent".
And then there's Ol' Myxie's second appearance, where he's banished to Earth for three months as punishment for his repeated torment of "lesser lifeforms" in the third dimension, and told that he'll get his powers back only if he's shown that he can perform good deeds for said lifeforms instead. Cue Superman putting Myxie in charge of keeping a look on Bizarro on the alien planet he left him on, complete with being forced to put his fake city together so Bizarro will have a place to "protect" and getting mauled by Bizarro's vicious alien "dog".
What really sells it is the fact that Superman is watching the whole thing from the Fortress of Solitude with the biggest, smuggest, most self-satisfied grin this side of Superdickery.
The crude cartoon Mxy uses to convince Bizarro that everyone in Metropolis is mocking him behind his back.
In World's Finest:
Joker: *abruptly busts in on a room full of gangsters* Caesar Carlini, my old pal! Why, I haven't seen you since... *pauses, thinking hard* Waaait. I've never seen you, have I? Wow, you need to get out more.
Especially with the fight beginning with Mercy doing a Dynamic Entry.
When Superman shows up to stop him from interrogating a thug, Batman grabs his arm and throws him across the room. The look of utter shock on Superman's face is fantastic.
Superman: You've got your information, now—. Batman: [grab, judo throw (letting go of the thug he was interrogating)] Superman: ... Batman: [notices thug running away, starts pursuit... only to be shoulder-slammed so hard by Supes that he crashes into the far wall] Superman: I heard you were crazy. I didn't think you were stupid.
Superman using X-ray vision to learn Bats is Bruce Wayne. Bats' response? "You peeked."
Immediately after this confrontation, when Clark goes back to his apartment and undresses for bed while having a phone conversation with Lois, when his super-hearing catches an faint beeping coming from his apartment. He quickly discovers that it's a Bat-tracer, attached to his cape. A quick super-scan out his window reveals Batman watching him (with binoculars) from several rooftops away, which means Batman now knows his secret identity and where he lives. Batman tops off this awesome moment by saluting before he leaves. Bad. Ass.
Harley's little rant as she's being taken away in a straitjacket to be shipped back to Arkham in the aftermath. And Mercy watching it on TV, getting the last laugh at her expense:
Harley: I want a lawyer! I want a doctor! I want a cheese sandwich! (is unceremoniously shoved into the van and they drive off) Mercy: (watching this all from back at LexCorp, in bandages by the way) Now, that's funny! Ha-ha-ha-OW!
Yes, Mercy actually hurt herself from laughing so hard.
Bruce's final words to Clark before he gets on the plane: "[Lois] is all yours now, if you can handle it. You'd better be good to her... 'cause I know where you live."
Darkseid telling Superman that he actually landed on Apokolyps as a child... While calling himself "kind" and the animation casting him and Granny Goodness in the role of the Kents. And Darkseid smiles kindly.
Clark: (lowers his glasses) Well, Lois, the truth is, I'm actually Superman in disguise and I only pretend to be a journalist in order to hear about disasters as they happen, and then squeeze you out of the byline. (beat) Lois: You're a sick man, Kent. Clark: You asked.
Speaking of the Main Man!
Professor Hamilton: I can't help wondering about civilizations on other worlds... their great achievements, their brilliant minds.... (cut to Lobo letting off a loud belch in a Wretched Hive)
Then he encounters Lois:
Lois: Get away from me, you sick pig- (slaps Lobo, finding out the hard way his skin is like rock) OW! Lobo: Ooo! I like a babe who plays rough! Come on babe! (points to his cheek) Let me have another. Right here, right- *gets decked by Superman and sent flying*
One gets the feeling that Superman is taking the opportunity to embrace the "man" part of his title; a stinky, drunk biker is pawing his girl, so POW.
Even better, this results in a "kid-friendly" continuous stream of profanity from Lobo... as Superman sent him flying through Luthor's office (already damaged by the fight), you see a very angry Lex Luthor, ordering his goons to....
Luthor: *ticked off* I want all repairs completed— *cue Lobo being thrown through Lex's office again—this time from the floor straight through to the ceiling* killrendfragdestroy—! Luthor: *even more ticked off* IMMEDIATELY!!
Pretty much everything that comes out of Lobo's mouth is hilarious, but the following is particularly funny in its delivery:
Lobo:Finally! I've been trying to get in touch with you all day! Superman: Who are you? Lobo: *deadpan* Oh, I'm sorry. My card. *Lobo decks Superman through a building.*
A subtle one, but when Lobo arrives in Metropolis, he makes the rather sensible decision to just ask where Superman is by walking into a police station and showing them his picture. Even better, the desk Sergeant barely bats an eye at the hulking white-skinned red-eyed guy who shows him a holographic three-dimensional image of Superman.... he just explains calmly that the police don't keep tabs on Supes. That either speaks highly of the professionalism of the Metropolis PD, or it's just that they see weirder stuff than Lobo on a routine basis. Then there's the way the conversation ends....
Cop: [Superman] only shows up when there's trouble. Lobo: I can do trouble. *racks gun*
A little later, while he's in the half-ruined police station waiting for Superman to show up:
Lobo: (yawns) "This is getting lame. I thought he'd be here by now. WOAH! MOSQUITO!" (Blam!)
During the fight with Superman:
Lobo: "Now, the more you move, the more this will hurt, so feel free to go nuts!"
Throughout all of Part 2, whenever Lobo winds up facing some sort of opposition trying to stop him he simply replies "Who's gonna make me?" only for said opposition to start smacking him around. When this happens near the end when he's confronted by the Preserver, the Preserver proceeds to transform into a red behemoth. Lobo realizes he may be just a bit Genre Blind...
Lobo: You know, I really gotta stop saying that!
Again in Part 2, Lobo and Superman are cornered by a trio of bounty hunters, leading to a laser gunfight in the Preserver's enclosures. The bounty hunters can't quite catch their quarry, so one of the thugs decides to taunt Lobo.
Gnaww: We followed your bike's ion trail! It was stronger than your breath! Lobo: Hey! Watch what you say about my bike! Whereupon Lobo takes a laser shot to the face and ends up briefly stunned and with a humorous Ash Faced expression. It's about the only time he's actually shut up by an injury, even if only temporarily.
In "Knight Time", Bane's "No way!" expression as Superman, dressed as Batman, beats the crap out of him with his bare hands.
Robin: (to Riddler) He's been working out.
The "That's it, no more mister nice guy" look Supes aims at Bane before applying the beat-down.
Then after that, screwing with the Mad Hatter using Super Speed. The "Oh Crap!" expression does not leave the Hatter's face once in that entire sequence.
Mad Hatter: Curiouser and curiouser!
And when Superman forgets himself and grins at Robin. It totally freaks out the Mad Hatter until Clark remembers he's playing Batman and scowls again.
Similarly, as Superman emerges from a fireball, his Batman costume burnt away:
Superman: Today's been full of surprises. *punches Brainiac*
Also in "Knight Time", when Tim Drake (Robin) asks Superman how he can imitate Batman's voice so well:
Superman: (doing Batman's voice) Precise muscle control. *Tim just smiles and keeps walking on until* Superman: (doing Robin's voice) Plus, I have a pretty good ear. Robin: (turns and glares at Superman) Don't. Do. That. Again!
And Robin giving Superman impromptu Batman-interrogation lessons: "Kick over the desk". This being Superman, the desk is less "flipped" and more "reduced to splinters". Penguin's "WHAT THE FUCK" expression sells it.
Really, seeing the Boy Scout pretend to be Batman was hilarious; it's a fun Lampshade Hanging on the limited amount of character models available at the time that Superman can pass himself off as Batman (who at least in the comics is usually quite a bit thinner), although a cop does ask Commissioner Gordon if Batman looks "bigger", because Supes' character model does have broader shoulders than Batman's in the DCAU.
How does Robin know something is wrong about the message Bruce left behind to explain his absence? Because he's smiling.
In "Warrior Queen", the whole sequence of Superman fighting Maxima is witnessed by an older woman. Her comments to her husband about everything going on, and her husband's responses to them...HILARIOUS!
Wife: Murray, there's a man and a woman fighting!! Husband:[not taking his eyes off the newspaper] Stop spying on the neighbors, Lucille.
When Maxina hugged Superman for actually beating her.
Lucille: Oh my goodness...now they're hugging. Murray: Don't get any ideas!
Heck, the reaction of Superman when Maxima expresses her joy that Superman beat her!
Maxima: No one has lasted this long with me - no one! You are...my equal! (Maxima abruptly hugs Superman) Maxima: This is the happiest day of my life! Superman: (dumbfounded) I'm...glad?
After Superman explains to Maxina about Earth's concept of love and marriage.
Superman: Here on earth, marriage isn't something you can command. Marriage is a willing partnership where husbands and wives share the decisions and sacrifices. Lucille: What planet is he from?
Plus, the out of nowhere cameo of Lobo. Naturally, it's love at first sight.
And then there's the scene where Maxima barges into the news room just as the newswoman had said they needed something to fill two minutes on the Superman piece they were doing. Maxima announces herself as "The Lady Maxima, Warrior Queen, head of the royal house, leader of all Almarec. And Superman's betrothed." The newswoman looks like Christmas has come early and simply breaths "Thank you!"
The scene after she's briefly subdued Superman, dragging him by the cape like a caveman.
And the scene where Superman tries to bust out of the prison, only to run into a forcefield and do a hilariously slapstick Faceplant upon landing.
If we count the redubbed Kids' WB! promo spots, I nominate this one using footage from the episode where Superman raced Flash:
Best part, in the beginning of the next episode....SHE DOES!
This bit from "Superman's Pal": So you know how stupid mooks always try but fail, every time... to shoot the Man Of Steel? Some villain tries to hit him with a bar. Superman naturally lampshades this, "You're kidding, right?"
From Bizarro's intro episode:
Bizarro: Me am Superman! Me am hero! Lex Luthor: Sorry my friend, but you am toast.
Also, Mercy's sarcastic reply when Bizarro asks who he is:
Bizarro: What...am me? Mercy: "Bizarro", that's what you am.
After Mercy's reply makes Bizarro angry and he flies off crashing through the roof.
Luthor:(to Mercy) That's coming out of your pay.
Not to mention Bizarro attempting to prove he is Superman by "saving" an abandoned building from a wrecking ball and "fixing" a lifted drawbridge just as a boat is about to pass through it.
After Bizarro throws away the wrecking ball crane, it's about to land on a wedding. Superman had only seen the crane fly through the air and not who threw it. After saving the people he simply says, "Don't ask me. I just catch 'em."
Lois: (looking at a picture of Superman) Nice "S". Clark: Excuse me?! Lois: Right here (Points to Superman's S-Shield)
Any time Granny Goodness speaks, thanks to being voiced by Ed Asner. Whoever made that casting choice is an insane genius.
In "My Girl" Lana Lang is getting ready to return to Smallville:
Clark: I know you'll find that special person someday. Lana: So will you; you deserve it. Someone quiet, understanding, patient— Lois: (From offscreen) Hey Smallville! Get your tail in here; Perry's got an assignment for us!
In "Monkey Fun", one of the escaped monkeys starts jumping on a little kid. His mother tries to get him off, but another monkey starts crawling on her.
Boy: Monkey, monkey, monkey!
Then the boy waves at Superman as he flies away. The monkey waves too.
Superman: I'm sorry Lois, but your monkey friend is going down. Lois: Don't hurt him, he's just a baby! (Jimmy looks at her) Okay, a really big baby.
When Titano is rampaging around the docks, Bibbo, because he's either really stupid or has giant balls (probably both), climbs on top of a stack of crates, slaps Titano with a newspaper, and calls him a bad monkey. Titano casually picks him up and throws him into a trash barge.
The ending of "The Late Mr. Kent" Has Clark call on Lana to help him fake not his "death" but his survival. She also uses the opportunity to screw with Lois and rub her nose in Lana and Clark's close relationship. The way Clark and Lana grin at each other after Lois leaves the room is just icing on the cake.
From "Unity," after Supergirl does all of her chores — including collecting eggs — at Super Speed:
Ma Kent: Now, Kara, you know how that upsets the chickens. Pa Kent: Good thing I didn't ask her to milk the cow. [Cue the cow's strangled mooing from outside.] Supergirl:[hefting a jug of milk] Oops...
In Livewire's debut episode a construction worker actually agrees with the pre-Livewire Leslie Willis' vicious attacks on Superman, believing the Man of Steel to be too nice to be real. And then this idiot construction worker almost causes a serious accident and Superman has to save him and a lot of people in the process. Looks like that guy had to eat his own words...
From the same episode the scene where after Leslie's been zapped and just about to activate her Livewire powers for the first time she's watching a news report and Superman is shown being questioned by reporters about the accident. At least two of them insinuate that Superman may have allowed Leslie to get fried on purpose in order to get revenge on her for all the trash talk she'd been slinging at him. As the second reporter reminds Superman: "She said some pretty awful things about you. Maybe this was your way of paying her back." It may not be intentional but it is funny.
In "Legacy Part II", when reporters ask people about their opinion of Superman after the invasion of Earth, Lex Luthor is shown wearing a neck brace, and saying "no one man should have all that power" with his jaw wired shut. It's the only funny moment in one big Tear Jerker of a two-part episode.