Lelouch casually pushing C.C into a truck filled with tomatoes when he sees Shirley coming... and then preceding to close the top on her.
Viletta's response after she is forced to wear a really skimpy swimsuit for a school festival when she was posing as a teacher in R2. Complete with eye twitching!
Shirley: "Oh, I'm so happy the coach agreed to do this for us!"
Viletta: (internally) "So help me, Shirley, you'll die a thousand deaths for this!"
The Cupid's Day chase, where Anya deployed her massive mech. The conversation doesn't read as funny as it is on the show, but Anya and Viletta's exchange was awesome when heard.
Viletta: Lady Knight of Six, this is the operation area of the Intelligence Agency. Please move your Knightmare Frame away immediately.
Anya (in utterly innocent voice): It's not okay?
Viletta: (almost facefaults): It's not okay!
Anya (sounding disappointed): It's not okay...
Not to mention she really has no reason to go chasing after Lelouch as everyone else does, being neither attracted to him nor a member of a club yet she still picks an extreme way to catch him.
Well... maybe. Between having a person looking very much like him in her past, and every other girl her age in the series being attracted to him, it's not that strange. It's not as if Anya would be half as obvious as anyone else about such things.
It's even better: the deployment of the mech leads to the entire nation entering DEFCON 2 and preparing for a terrorist attack.
The best part of Cupid's Day was when Sayoko as Lelouch ran past the Seduction Squad and yelled "Your bodies are of no interest to me!" All of the girls are stunned (despite the fact that Lelouch has been completely asexual the whole series) except for one who says halfheartedly, "Huh, I'm kind of in shock."
The entire sequence of Sayoko running around as Lelouch is comedy gold because of how over the top it is; actually asks her to "please stop making me say strange things" (but not in response to the above line, sadly).
The dub made it even funnier. As Sayoko/Lelouch avoids what looksl like the school's rugby team, she jumps off of them yelling "Fare thee well!"
Lelouch also mentions how it's pointless for him to commande Sayoko to stop since that's just how she is. However he can think of one good thing from this:
Lelouch: Oh well, she can take my place in Phy. Ed from here on.
It even manages to sneak one into the "Where Are They Now?" Epilogue: Jeremiah "Orange-kun" Gottwald works on a farm...growing oranges. This is even more hilarious when you consider that, way back when, he chose demotion as a punishment over being forced to work on an orange farm.
Suzaku: Thanks! I wore one for talent night in the Army!
Near the end of the Chinese Federation story arc, Diethard suggests arranging a political marriage between the Chinese Empress (who they just saved) and one of the Black Knights. Before Lelouch can offer his two cents, one by one every single high-ranking female Black Knight rejects the notion and calls Diethard an idiot, stunning even Lelouch. This includes the normally stoic C.C., militaristic Chiba, and lackadaisical Rakshata. And then Zero dodges the issue by acting like Tamaki is important.
And before that, Zero's ridiculous pose when he assured Tianzi that she will not be a puppet of the Black Knights.
"The thing with Lloyd is... so many things are wrong with him as a human being!"
"...They're using a Knightmare frame to make a giant pizza?" - Gino
Jumping back to the first season, when Lelouch and Euphy are stranded on an island, he attempts to dig a pit trap to catch some of the local wildlife while she volunteers to gather some fruit. Of course, due to his physical unfitness, he can't even manage to get a two-foot hole. Time Lapse to nightfall, where they have lots of fruit and no meat, and Lelouch has an absolutely pitiful expression on his face, which is what really sells the scene.
The show's school festival episodes are all hilarious before the final five minutes dip back into seriousness. This includes the first two examples (from R2 episodes 5 and 12 respectively) as well as "The Stolen Mask" and "Declaration at the School Festival" (episodes 6 and 21 from the first season).
Speaking of episode 6, the girl who randomly said that she wanted to kiss Milly. The reaction was simple: "Now is not the time to come of the closet".
World's largest pizza.
C.C.'s reaction to said pizza flying into a tree was priceless.
"Please note that this contraption at my feet is an oven specially built for this occasion; a fabulous waste of money!"
Another thing from episode 21. Lelouch gets Kallen to go help with the festival's haunted house. This results in Kallen dressed up in a horrible-looking costume with her face painted red, popping up out of a hole in the ground yelling things that she's apparently thinking as she does.
When she scares Ohgi - she realises it's him, and both of them are fairly mortified by the situation, with the tone of their voices all but saying "Let's never speak of this again."
Two funny scenes involving Kallen were put into the manga adaptation:
During the school festival in R2, Lelouch starts out in the chubby mascot costume, but switches with Kallen, who uses a voice-changer to sound like Lelouch. Then Shirley and a swarm of Lelouch fangirls show up and demand that "Lelouch" take of the costume, and Kallen winds up being chased all throughout the rest of the festival.
Later, when C.C has lost her memories, Kallen is assigned to take care of her. After giving C.C. a pizza, she tries to strike up a conversation, but C.C ignores all in favor of eating the pizza. This makes Kallen flash back to when she and C.C were living together after the Black Rebellion, with C.C being a total brat and ordering her around. The next panel shows Kallen with an angry look on her face holding the pizza out of the reach of C.C., who's crying and trying to get it back.
The same manga has a bonus chapter (in vol.6 of the US release) which is almost entirely CMOF. Kallen enters Lelouch's room while he's doing repairs to the Zero costume (with C.C. munching on pizza nearby) and he struggles to hide the incriminating evidence. But the crowning crowning moment comes when Lelouch is covering Kallen's eyes; C.C. pokes her head out from under the bed, then goes for the Zero mask, while Lelouch thinks "Good! Hide the mask!"...and then the next panel shows C.C. sitting on the couch, wearing the mask and holding a glass of wine, to Lelouch's utter shock and frustration. Just as a cherry on top, she spends the entire rest of the story with the mask and wine.
The episode with the Elevens dressing up as Zero. The first time we see the Zero clones, a dog wearing a Zero mask is clearly visible in the foreground.
In the same episode, Tamaki (dressed as Zero) motivates the other Zeros to join them in their exile. Clearly he picked up a lot of Zero's exaggerated mannerisms.
During the first school festival in R2, during the chase after Arthur. This includes Suzaku, Milly, who's chasing him, Kallen in the above chubby mascot costume, and Lelouch. Kallen and Lelouch are chasing after the Ganymede, which is holding a tub of tomatoes with C.C. inside after Lelouch pushed her in there. Gino, who takes control of the Ganymede, nearly runs over Arthur while on the road to the place where they're baking the giant pizza. Suzaku, who's supposed to be piloting, is chasing Arthur, who grabbed a quill pen that used to be Euphie's.
Milly and Lloyd's "blind date" scene. Her shyness/weirded-out expression plus Lloyd's total Cloud Cuckoo Lander attitude ("Let's just get married!") makes it. The scene a couple episodes later where he bursts unconcernedly into the student council party and calls Milly "honey bunch" (at least in the dub) is also fully worthy of mention.
Rivalz horrified response when he learns just who Lloyd is is great:
Rivalz: "Milly, who is this guy?"
Milly: "Rivalz, this is Earl Asplund."
Rivalz: *Double Take* "Earl?" *bows* "It's an honor, your lordship. Now... what did you say your relationship was?"
Lloyd: "We're betrothed."
Rivalz: *collapses in tears*
Mao's second episode, where he kidnaps Nunnally. Before he shows up, Suzaku and Lelouch are talking outside the school, only to be interrupted by Rivalz, who asks about when Milly's blind date with Lloyd is. Lelouch replies that it's today, and Rivalz freaks out, saying "TODAY?! WHY DIDN'T YOU TELL ME ABOUT IT!?" combined with a collar grab. Lelouch calmly responds "Because it'd make you cry." Rivalz responds by saying boys don't cry, and when Suzaku tries to cut in, he yells "Don't give me your emo routine!" to which poor Suzaku says "Emo?" in the most innocent voice, complete with confused blinking.
Which is even funnier if you consider that Suzaku's English voice actor also plays as Sasuke from Naruto.
Lelouch's line "Cats and tomatoes don't mix". JYB's delivery of the line is so serious it's hard to avoid laughing at this point of the episode.
A very subtle moment was when the Black Knights were taking refuge in the Chinese embassy. C.C. and Kallen were talking while repairing guns and C.C. is unable to fix hers, and it flies out of her hand while she's in mid-sentence, then she picks it up and continues talking like nothing happened.
"Code Geass Hangyaku" from the DVD which showed Sayoko's first meeting with Suzaku and her initiation into the Black Knights.
The conversation between Zero and Jeremiah in the season 1 finale:
Jeremiah: Mr. Zero, can it really be? What? Oh, what luck, what fate, what evil fortune!
Zero: Is that you, Orange boy?
Jeremiah: I beseech you! I'm begging you, please die.
Lloyd has one in the 7th episode with the saying, "Alright everyone, pack it up, pack it up! We're done today. Don't do anymore. Hip hip hooray! That's all folks."
Lloyd in general is just really funny, such as when he's supposed to be signing mountains of paperwork for Suzaku to take part in an execution:
Guard:(panicked) "What's going on?"
Lloyd: "Oh good! We're free of all this hellish paperwork."
Or when he sees that Rakshata has perfected the Hadron cannon in Episode 20 of R1:
Lloyd: "They made the beams converge!? But I wanted to be the one to perfect that system!"
Or when Milly guesses his real reason for wanting to marry her:
Cecile: "You've finally got it. He has no attraction to the opposite sex whatsoever."
Lloyd: (sidelong glance) "Oh, I understand the principle well enough..."
In C.C's first proper episode, when Lelouch spots her in his school when talking to Kallen he grabs her head and turns it back to him to stop her seeing C.C, that's not the funny bit, this is:
In an incident with Cecile's cooking in episode 7, Lloyd accidentally eats one of Cecile's sandwiches and runs off, presumably to the bathroom. This in itself is not the funny bit; what is funny is that the normally stoic Guilford makes the most disgusted face when he watches Lloyd put that thing in his mouth.
During R1 when the Black Knights are in their hideout, Ohgi brings Zero a letter. The conversation goes something along the lines of this:
Zero: What is it?
Ohgi: ...It's a love letter...
Zero: From YOU?
(cue Tamaki laughing insanely)
Kallen: You laugh too much.
Emperor Charles saying Lelouch's name in the anime sounds more like he's impersonating a car engine.
Right before C.C. runs off with Marianne (Anya) to flee the Black Knights, she says she has to go grab something first. When you later see her in the Mordred, she's holding Cheese-kun
Shirley finding out about Lelouch being set up with 108 dates. Cue a very frustrated look on her face and an epic Say My Namenote or maybe it's just epic because this is Shirley
After C.C. loses her memories and reverts back to her slave days, Lelouch seems to forget about this fact at the beginning of the next episode when he jokingly commands her to sing him a song while hopping on one foot with her clothes inside out and then being shocked when she actually starts turning her clothes inside out.
In a bit of meta-humor, episode 18 of R2 has Suzaku on the wrong end of a Curb-Stomp Battle with Kallen. Everything he tries is easily defeated, and he finally tries to close in with his patented Spinzaku kick. Kallen uses the Guren's wing to cut the leg off. This is when Suzaku decides he's screwed. Not when she blocked dozens of Hadron Cannon blasts then destroyed the blaster. Not when she broke right through his shield with her claw and destroyed the arm. No, it's when his signature move fails that he loses hope.
The scene in R2 episode 12 where Shirley calls out Lelouch for being a womanizer (actually Sayoko's doing) while the entire student body watches
Nunnally in Wonderland
Given its premise, it's expected that this OVA would have its moments. But did anyone really expect to see Charles vi Britannia as the King of Hearts, complete with a crown covered in giant red Valentines that flash like neon lights? And then there's the end, where the cast gangs up on Lelouch for Geassing them into acting out the story, culminating in him being dressed up as The Mad Hatter. Complete with a fabulous outfit and requisite hammy laugh.
Lelouch's constant side-comments that only slightly exaggerate his overprotectiveness and devotion to his beloved baby sister. From lamenting that if he could shrink her and keep her safe in his pocket, he wouldn't have started a world war for her....to scolding her ("This Is Unforgivable, Nunnally!") for daring to think about finding a husband, and vowing to prove that he can take care of her for the rest of her life! C.C., true to herself and her character, lampshades this, even going as far as to call Lelouch "controlling". And since she's immune to Geass, one can only wonder if it really is being played up for laughs...
Anya/The White Rabbit challenging Kallen/The March Hare for the role of cute mascot of Wonderland.
The battle between Suzaku and Gino (the White and Red Knight respectively) is shown with paper dolls. It ends with Suzaku spinning his sword so fast that he flies, then unleashing an ultimate Spinzaku kick.