Pretty much everything happening in the background of the student council meetings. Knife throwing acts, restaurant tables and the student council eating the bills, mikes and cameras appearing from nowhere when Saionji asks Touga an Armor-Piercing Question, a train crossing with an invisible train that covers what they're trying to say...
Nanami's various attempts at trying to embarrass Anthy in the fourth episode by trying to make it look like she keeps disgusting animals in her room. Only to have them horribly backfire because Anthy is already doing stranger things than the ones Nanami is trying to pull on her, such as keeping snails in her pencil box (compared to Nanami's single snail), a mongoose in her desk (that ate Nanami's garden snake), and a gigantic octopus float from the school festival in her closet (Nanami wanted to put there a much smaller live one). Nanami's desired results:
Miki: Miss Himemiya! I've misjudged you! Utena: I'm so shocked!
The actual results:
Miki: I think it's cute. It's just like Miss Himemiya to do something like that.
During her duel with Utena, Juri shouted “There are no such things as miracles!” as she disarmed her. Immediately after that, Utena's sword fell down from the sky and cut out her rose, giving Utena the victory.
Juri's WTF face as she registered what had just happened.
Dub!Utena's snarky response to Saionji obsessing over his love with Anthy in episode 6.
Saionji: For example, the love Anthy and I share is hidden love. * beat* Saionji: That's hidden love. Utena: Yeah, nice skirt, Saionji.
In the original Japanese, it's even better:
Saionji: For example, the love Anthy and I share is a hidden love. * beat* Saionji:Hidden love. Utena:Nobody asked you.
The scene is made even better by the long and awkward silence whilst delicate piano music plays in the background-and by him showing an exchange diary, of all things, when he mentions hidden love.
In Episode 8 Nanami and her cohorts go to India to find the nine-billion fold curry to reverse Anthy and Utena's Personality Swap and encounter elephants everywhere.
As they cross a delicate single-rope bridge an elephant rampages towards them.
While they're in the sea a whole wave of elephants on surfboards wearing sunglasses turn them over.
Anthy!Utena gets glomped by Wakaba, and promptly slumps to the ground.
Nanami's Girl Posse try to bully Utena!Anthy, who responds by slapping one of them back and challenging them to a real fight.
And in the finale, they are successfully able to unswitch Utena and Anthy's Personality Swaponly to cause one between Saionji and Chu-Chu.
Even better was that Utena and Wakaba just sighed while Anthy looked absolutely delighted.
Anthy!Utena's Eye Twitch at what Saionji wrote about her and what she wrote to get back at him: "Dumb Ass". Especially when we see Saionji's reaction.
The fact Saionji keeps an exchange diary with Anthy... And that it's actually a Brick Joke from episode 6.
Anthy!Utena believing Touga to be responsible for the body switch, to which Nanami proudly declares "This whole thing is my doing!" She then gives out a big Noblewoman's Laugh while Keiko, Aiko, and Yuuko make shushing noises to get her to stop. Nanami then has to switch gears and bullshits to Touga that she just wanted to help Anthy make good curry. Anthy!Utena's expression basically says "Bitch please."
Nanami's posse took pictures of Anthy!Utena and Utena!Anthy for Nanami to try and understand what was happening... And they also sold copies to the whole school. Both sets were popular with both genders.
Miki lamenting of the switch... And that he couldn't help but buy the pictures of Utena!Anthy.
Touga shows up, scolds Nanami for the whole mess... And does the thing he was actually there for: buy a copy of the pictures' negatives.
And all of this happened because Nanami decided to slip Anthy an ingredient to make her curry super-spicy and accidentally got one so spicy the package guaranteed to blow the eater to smitherens-and it actually exploded during preparation... But her posse forgot to switch the ingredients. Meaning it was all Anthy's cooking.
The manga has its own version of the curry episode, which lacks Nanami and thus her subplot, but has its own different funny moments.
The Student Council meeting that Touga holds after learning about the (curry) explosion in Utena and Anthy's building.
Touga: The Rose Bride and her betrothed - someone planted a bomb? This is the worst crisis ever to befall the Rose Seal. Who could have caused this? Who did it, and for what?!
Juri: Um, Student Council President...
Miki: Touga... they're both okay. The hospital released them.
Touga: Oh... well, good.
Chu-Chu writes the message to Saionji in the Exchange Diary (while dressed as Anthy) instead of Utena/"Anthy" (something Utena actually considered in the anime).
Chu-Chu: My deear Saionji, I'm sorry this is so late. Today I'll rite about Anthy's favorite foods. Banana. And cookies. And sweet potato. Apples.
Kanae: Please, won't you start calling me "Sister," now? It won't be long until I really am your sister, okay? (beat) (beat) Anthy(with the same vacant smile she always has): Sure.
Earlier in that episode, Utena and Anthy looking for the latter's older brother. Apparently in an overestimation of Anthy's Cloudcuckoolander tendencies, Utena asks if the giant projector is Anthy's brother before they find him.
Episode 16. Nanami shows her party guests the "luxurious" gift she was sent, only to reveal... a cowbell. And then she wears it to school.Proudly.
In episode 22, the Student Council's meeting place has a train crossing. And the invisible train covers what Nanami and Miki were trying to tell Juri.
Nanami's Egg, full stop. Also the three nerdy guys, whenever they appear.
"Nanami, do you know the reason why we're so happy together? It's because you aren't the type of girl who would go about laying an egg. Pity the poor parents of a girl who would do something so shameful as to lay an egg." It gets funnier (or perhaps just shows once again what a jerk Touga is) when you liken girls laying eggs in this case to teenage pregnancy, and realise Touga's hypocrisy from there as you wonder just how many girls he might have gotten pregnant.
Another one! Nanami beating the crap out of Saionji when she thinks he's cooked her egg.
Saionji just showing up randomly in the woods because he felt like a spot of camping.
Then of course there's her Imagine Spot after she meets Keiko, Aiko, and Yuuko. When's she finished she shouts "I won't go with them when they come to take me away, I won't!" The girls have no idea what she's talking about before Nanami inches away nervously/psychotically.
Keiko: Miss Nanami, are you all right? Nanami: Oh it's nothing, nothing at all! La lala lala lala lala!
The "Three Wishes" sidestory in the manga. Giant Saionji, anyone?
I've got a fever, and the only thing that can cure it is more cowberu.
Forget cowberu. What you need is more nose ringu.
Most of C-Ko's shadow plays in the second season.
From the movie, any mention of F-Ko's "scandalacious" videotape. I mean, until we actually see what makes it so scandalacious.
The "Nanami Cow" segment.
Touga and Saionji in the motorcycle in Episode 36:
Touga: Saionji. Saionji: Yeah? Touga: Standing like that is dangerous. (beat) Saionji: Right. (sits back down)
The whole scene is just perfect. Throughout the entire arc Akio's sports car is a huge allegory for sex, power, and "adulthood" as a teen thinks of it. So then Touga takes Saionji riding down the same highway...on a tiny motorbike with a sidecar. He attempts to imitate Akio's speech and mannerisms, only to fail spectacularly, and the whole thing is just so obviously him trying so hard to be a real grown-up and getting it wrong.
How Wakaba always tries to glomp Utena when they're both in front of an open window.
Wakaba's Genki Girl status makes her quite hilarious. In particular, there's the beginning of episode 11, where she glomps Utena and causes them both to roll down a hill.
The second Ruka episode hangs an amusing lampshade on the Stock Footage used in that arc. Ruka does the usual speech that Touga normally does in the leadup to the Akio Car scene... except for the last part where the car appears, at which point he calls Touga in just to say his last line and do his overdramatic shirtless pose.
And Touga is still so happy about saying his line.
Also worth a chuckle is a giant Chu-Chu kicking over the Akio Car. It pops up again in the Chu-Chu joke ending, too.
Anthy's joke ending, oh so much.
"Don't you just love the throb of the engine?" It's not an uncommon line in the Akio Car scenes, but it turns into an ungodly Freudian Slip when Ruka and Shiori have sex on the back seat. Worse still, the line has also been translated as "She's purring nicely, isn't she?".
Oh, that's totally deliberate. Akio's car is a clear stand-in for sex. Which makes that scene more horrifying than anything.
From the movie-manga: Juri stubbornly refusing to watch Utena's duel against Touga because she's pissed that she's not the one duelling against her. It's funnier when you remember that Juri and Utena did duel in the actual movie. Oh, the irony...
Despite the episode with Mitsuru's diary about Nanami being a mostly filler Clip Show episode, there is that part with his plan if Nanami ever gets amnesia.
Mitsuru: Nanami, I am your big brother! Nanami (in joy): You're my big brother?!
In the same episode we see that Mitsuru had been stalking Nanami from well before his official debut-and even followed her to India during the events of episode 6, also being the source of the banana whose peel Chuu-Chuu threw to make Nanami slip.
Again from the events of episode 6: those three guys too ate the curry (in fact they did it before Utena and Anthy)... Alongside three elephants. For the rest of the episode there's around three elephants with those three guys' distinctive hairstyle and glasses.
At the final episode, after all the Tear JerkerMind Screw; in the final view for Ohtori Academy, those three guys trying to give love letters to Nanami's Girl Posse and being rejected.
Guy 1: Will you...~? Guy 2: Will you...~? Guy 3: Will you...~? Girl Posse: Hmm~! *rejecting* Guys: Aaah~...
Also, Wakaba at the receiving end of an overexcited glomp.
This might be unintentional, but just how easily all the guys in RGU lose their shirts. Every time Touga shows someone the End of the World his shirt just inexplicably flies open for no good reason.
Akio doesn't escape unscathed either. His shirt tends to explode open, followed by him doing a handstand on the hood of the car, after which he poses as if he was in a racy calendar, draping himself across the hood. It's so ridiculously over-the-top.
C-ko's shadow plays in the Black Rose saga, with Utena giving her snarky replies; but the funniest must be episode 19's, where C-ko bought small tires thinking she could make dinner with them.
Utena: Are those even edible? *beat* C-ko:(let the tire sac fall to the floor, in shoock)
The final "Next Time" preview segment, unlike every single one before it, chooses to replace actual plot hints with the Shadow Play Girls clearly not caring about their job, saying that Utena's problems will be conveniently resolved by miracles because it's an anime, and ends with "Oh yeah, the absolute destiny... whatever."
Similarly, the Next Time for Nanami's Egg also parodies other Arc Words by having Anthy say "If we cannot break the egg's shell, the omelet will never be made."
In the manga, Utena's getting very bad vibes from Touga and the duels as a whole while in the Rose Garden, so she grabs Anthy and runs away from Touga. Anthy wasn't finished watering yet, so she comes back to open the door and asks Touga politely if he would finish watering them.