In episode 3, Naru and Ao search the remains of her home for Noah and find him hiding in her underwear drawer.
In episode 4, Ao figures out how to deploy the Nirvash's handheld machine guns from its shoulders mid-flight... Except back in episode 2, he used the left arm to impale a G-Monster, so that gun goes tumbling into the ocean.
Elena quoting Rei Ayanami from Neon Genesis Evangelion, even adopting Rei's deadpan expression. And then when Fleur tells Elena not to quote comic books, Elena responds that she's not quoting a Manga, she's quoting an anime. This is actually funnier if you know of Evangelion's odd subversion of Anime First - namely the manga came out first, as an advertisement to the anime, which is similar to what occurred with Eureka Seven AO's manga.
Noah's antics in episode 5. He can move fast when he wants to.
In episode 8, Ao heads to a random bar to sulk. The owner is sleeping on the counter, while Noah pokes at him.
Ao and Fleur's ridiculously self-assured walk near the end of the episode, which is made funnier by their smug faces and complete ignorance.
Totally out of context but: "Let's show it to America and our stupid President!" Even if you disagree with that assessment, you will laugh.
Gazelle's passport picture in episode 9.
Gazelle manages to be the first character to draw Truth out of character when he loses control on a hillside road and plunges down the slope... right into the car that Truth is talking to Lt. Nakamura in.
Episode 12: Truth's almost out of character moment with Lt. Nakamura's cigar smoke ring and look of surprise when he finds that he cannot actually catch it.
Georg tries to get Ivica some coffee in space. He ends up shooting a water bottle and the mix pack at his head. "This is why I hate space."
Eureka gets Ao a change of clothes so he doesn't have to walk around in his pilot suit. Said outfit is the goofy track suit the crew made Renton wear as a joke in the previous series
Episode 14: Elena is about to ram Eureka when Truth moves in. The looks on both their faces is hilarious.
Noah once again reading a book when Ao and Doctor Fukai are talking.
When Ao learns that Naru just happened to show up when he came back to learn more about his mother, Fukai tells him to act like he came for Naru. What's the first thing (paraphrased) that Ao says? "I just happened to be here." Fukai just shakes his head. Not very smooth, Ao.
Christophe Blanc bashes US coffee in episode 16, then tries to get Ivica to pick him up some South American coffee beans since he's in the country.
When discussing the after effects of Ao's Wave Motion Gun, Stanley cuts in to mention that he named it the Quartz Gun. The reaction of the others can best be summed up as, "Ok, we're kinda busy discussing the important things."
While Ao is with Tanaka about Eureka, Noah is eating candy from a bowl. At one point he throws his head back and then does a Face Plantinto the bowl.
In episode 19, Elena is downloading a movie (translated and with all the special features) when a blackout hits at about 95% complete. She takes a couple seconds to react, but when she does her face is hilarious and her scream is heard by Fleur, who has a look of "not again."
In episode 21, a new Scub appears and a Secret (the same type from the pilot) appears to destroy it. Boy is it surprised when three Secrets are already there. Then they blow it up, which isn't as funny, but for a moment you can almost picture the Secret thinking "What the?"
Someone finally comments on Eureka and Renton's Deface of the Moon. Eureka's quick look of embarrassment says it all.
In episode 22, Ao's constant blushing and putting his foot in his mouth with Naru.
Ao finally mentions the horn-like objects that have been sticking out of her head since she started communing with the Scub Coral. Naru simply pulls them off, showing that they're just Hair Decorations.
Everyone important on Okinawa is listening in on Ao and Naru, and Naru's sister asking their grandma if Naru and Ao have kissed yet. Grandma isn't sure if they ever will.
Elena's reaction to the Secret head getting installed on her IFO.