While the Star Wars-strips dedicated to pointing out why Coruscant wouldn't work in Real Life was funny by themselves, the Crowning Moment came when the Overly-Long Gagwas interrupted.
Captain: Arrr! Take that, ye scurvy equine. And that!
Later, the same Doctor completely owns the Seventh.
Fourth Doctor: Well... I'm sure I can come up with something. Seventh Doctor: Heh heh... you mean you're sure we can come up with something. Fourth Doctor: No.
The author's outdone himself again, with Da 10 Docs, a Doctor Who crossover with Looney Tunes. Wile E. Coyote plays the Master. That is all.
Fourth Doctor: When the time comes, and you know the end is near... When you're down to that final moment and you know it's all over and regeneration is about to take over... I want you to punch yourself right in the nose.
And he's at it again with A Time to Kill. Four strips in, and Ten has just totally blown 007's cover.
Tenth Doctor: How's life in the SECRET SERVICE treating you?
Halfway through the Abel's Story side-arc, which featured by far the darkest, most serious material in the strip and went worse from there, the author created an "intermission" image while on medication. It features herself in her "Wiku Worm" sleeping bag, her mascot/sidekick Fluffy, vicious Psycho for Hire Aniz, and one tentacle of a creature Aniz horribly murdered. And (archived thanks to a quick-thinking forumite) it looked like this◊.
Edward Cullen: Oh, cherry cheesecake... you are my life now.
In Pokémon-X, Brendan accidentally walks in on May when she's changing. The following conversation ensues:
May: This peeping tom saw my breasts! Brendan: Agh! You've ever thought of closing the door when you're changing? Or maybe... wearing a bra?! May and her mom: What's a bra? Brendan: ! ...I'm gonna love this place!
"Contrary to whathe claims, I have a graph here that shows a line clearly going up."
Real Life Comics: after the conclusion to a relatively serious plotline, Tony, a Mad ScientistGadgeteer Genius, survives a nuke, atmospheric re-entry and a fall from orbit. He explains to the rest of the cast that he used his science to make himself completely invulnerable. As he puts it, "I'm not bullet-proof... I'm just proof.". What he says next kills this troper:
Dave: And you don't think this is a tad overpowered?
Tony: Hell, are you kidding? It's way overpowered! It's ludicrous for one person to possess this much power! I love it.
Later, Mega Man tries to claim that he was making a soliloquy and no one else should've been able to hear what he just said. Roll's response is priceless.
Roll: Thou can sucketh mine salty salami, Shakespeare.
Obviously this is completely subjective since the strip is generally very high-quality. This Troper laughed for a very long time after seeing this one.
The Wotch has plenty, some good examples that stand out being the Sonja subplot of Date Night of Doom and most times Cassie flips into Stalker with a Crush mode. Also, Sykos in general.
The spinoff Cheer! has 32's actions leading into and during the basketball game that wraps up the first storyline, as well as the similarly-timed Burger Fool storyline with Lindsay and the main girls.
Looking for Group has quite a few of these, mainly from Richard, but this troper personally believes that this page may be one of the very funniest: "You got Dick Roll'd."
This might just be me, but I found the thing the dwarf says in this issue to be pretty funny.
Dwarf: If ye let me out, troll, I will find some dirt for to eat. Mmm. Dirt.
"He is my mother." This troper burst out laughing. Especially the beat panels afterwards.
Lawyer:What?
Richard: What?
There's one early on in the comic
Richard: Do you remember the guy that kept throwing daggers at me? These are his teeth.
Jack is consulting with Parson, saying that he's the Only Sane Man in this land of battle-mad Royals. "Perhaps you should defect, and join us all.". Then Parson reveals his latest exploit in order to save Wanda's and Jack's lives:
Parson: It involves turning this battle into a food fight.
Jack: I see. Well! Bravo Lord! T'was a splendidly speedy defection.
"Are you questioning my logic?" Doubles as a CMOA.
Sluggy Freelance has so many funny moments over the course of its long run, but in this troper's opinion, the height of hilarious absurdity has to be the "Magic Flap" arc.
"My name is Gunman Stan Mckurt...and I shoot evil in the face."
"Now THIS looks like a job for emergency pants!"
"You know what the problem is with nudist colonies?" "Shoot." "No quality control."
"RALPH!" "Ralph?" "Yeah, I was thinking of changing my name from Murdock to Ralph."
And then she dies in this scene, and quite clearly reveals her shapeshifting capability. Wow, there are shapeshifters in the Star Wars universe! We've been shown that fact quite explicitly. Surely this will become important later in the plot. Only it never does. It's never mentioned again anywhere else in any of the movies. I think Anton Chekhov just committed suicide with his gun.
For added amusement, the next strip has Palpatine saying he went through Jedi training, and warning Anakin that the midichlorians he was treated with can raise awareness too far.
After Queen of Wands ended, the character Kestrel showed up in Something Positive only to get hit by a red car. This spawned a short meme in several webcomics (for instance, two characters from Checkerboard Nightmare were in the car). And then the mostly-defunct Absurd Notions updated... with the author putting up an ad indicating he was selling his car, which was red and had a "slight dent in front". This turned out to be completely coincidental.
This troper finds the panel right before that conversation to be even funnier.
Bailiff: Do you solemnly swear to tell the truth, the whole truth, and nothing but the truth, so help you God(s)?
Zexion: No.
Namine and Riku in the hula competition. They opt to do their routine to Rock You Like a Hurricane. Less than a minute into it, an announcer informs everyone that the competition is a charity event with the proceeds going to Hurricane Katrina victims.
Klaus's entire list of demandswhen he takes over Attica. "Number... um... four? The sun will now rise in the North and set somewhere between Kansas and Budapest promptly before my bedtime. As a contingency, if the Sun refuses to comply within three days, wherever the sun rises will then be deemed North, and I may in my infinite mercy be willing to negotiate the bit about Budapest."
This Troper has to give out a mention to this strip of Touhou Nekokayou. I point specifically to the punchline. Even though that CSI: Miami joke has been used before, it was particularly awesome this time because of the shadow of Hisou Tensoku still looming. That, and the "fallout" pun really got me for some reason.
This exchange from the Create.swf Adventures spinoff:
Daiyousei: Yeah, you got me there. I have a birth defect — I'm actually intelligent, it's why I'm called Daiyousei.
Pretty much the entirety of the webcomic Shark Attack!. The comic itself consists of a shark attacking someone in a different way each time. This troper's personal favorite is when the shark drops a toaster in some guy's bathtub.
The first Christmas comic for Exterminatus Now has Lothar Hex getting a lifetime supply of Jack Daniels. He drinks it ALL and is seen hugging Blasphemy while saying that he'll be "The besht king of the woodpeckers ever!"
Eastwood's creepy obsession of his ex-girlfriend, up to and including his I Meant to Do That dealing with her new daemonologist boyfriend.
Luke'sfourteen-pagespeech/rant/deranged series of revelations after he comes back from the grave with a gaping hole in his head. He hams it to heaven (with appropriate poses), the others keep interrupting him (to his disgruntlement), it's impossible to ignore the lovingly detailed and gory hole through his fucking head (which he complains about, along his visions beyond death being figures wreathed in glorious light and deific sound who said to him, "Luke, you're still a complete wanker,"), until KK finally gets fed up with his blithering and knocks him out with a chair. Miki draws a penis on his face while he's unconscious. It's all just...wonderfully silly. And well-deserved.
Adelaide: Look. You're some halfwit who thinks he can take on vampires with a hammer, a pussy, and a zombie. I'm not exactly threatened. And I have better things to do so go away.
Hanna: Whoa. She just called you a pussy. Sorry dude.