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
And in the finale, they are successfully able to unswitch Utena and Anthy's Personality Swap only to cause one between Saionji and Chu-Chu.
From episode 14:
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.
"To be an adult.. you need experience in certain things".
"Oh Miss Utena, I believe you and I have done some adult things."
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!
Episode 8, "The Great Curry High Trip". You will never look at elephants the same way again afterwards. And at the end of it, Saionji and Chu-Chu switch personalities.
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.
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 the things Nanami is trying to pull on her, such as keeping snails in her pencil box, a mongoose in her desk, and a gigantic octopus float from the school festival in her closet. 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.
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: Standing like that is dangerous.
Saionji: Right. (sits back down)
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.
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?".
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?!,
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.