It's unintentionally funny, since the scene is anything but funny, but Mink coldly wondering why Aoba cares so much about his AllMate since they're just machines, when his own AllMate is greatly decorated in a manner that could only be done by him, counts as quite the Hypocritical Humor.
There's a scene early on in the game were Noiz breaks into Aoba's room, and as they're arguing, Koujaku ends up with them too, and Clear joins as well by rising up from the bottom of Aoba's window and basically breaking in. This almost seems like it could've been a serious scene, but then Granny breaks up the fight, and they all end up in the kitchen discussing their dispute over donuts. And Let's not forget Clear's "MAAAAAAA-SUUUUUU-TAAAAAA!"
When all the main characters discuss about Tae's whereabouts, Clear says that he knows the area's layout. Due to his behavior, none of them believe him. Clear notices this and is clearly dismayed, and draws a map of said area — which looks like a child's scribble. However, when Noiz confirms it to be actually accurate, Clear is all the more chagrined that they didn't believe him.
Near the end of Noiz's route, it turns out that Mio, of the three bratty kids, has developed a crush on Noiz. The way she shows this is by handing him a love letter written in crayon, and then angrily saying that he didn't have to read it. Both Noiz and Aoba are clearly at a loss.
Another Clear moment: He calls Aoba at Platinum Jail, having found a secret entrance to Oval Tower. Aoba follows a map provided... only to find it was actually a place named "Overr Tower".
And prior to that, when Clear tried to make Aoba feel better by preparing him food... while wearing nothing but an apron (and his gas mask).
In RE:Code, he's not completely naked and wears a pair of boxers, but the scene remains just as hilarious.
During a walk in the Green Playground, Noiz purchases various types of food, not knowing what they are. When Aoba asks what he's been eating, Noiz nonchalantly replies he's been living off delivery pizza and pasta for the last few years.
As shown in the page image: the second Aoba looks away, Noiz steals one of his takoyaki with the most serious face in history.
Aoba's constant irritation of Ren being taller than him in Rhyme and in real life as Sei despite Sei only being 1 cm taller!
Aoba imitating one of Koujaku's many fangirls in the drama CD.
"I failed to be the 'top'.", said by Aoba in Ren's route.
In the drama CD, Clear attempts to impress Aoba by trying to act as the "perfect lover"... and acts completely out of character by trying to appear manly and suave, then when exiting the shop in said manner, accidentally hits his face against the door. Needless to say, Aoba is left dumbfounded.
In the following track, Aoba suggests that Clear call him by his name without using any honorifics. Clear's completely embarrassed reaction is both adorable and hilarious.
Equally funny and heartwarming: in the drama CD, Aoba prepares a special dinner for Mink. Mink notices this, and Aoba makes him guess why. Before he could even give a hint, Mink immediately answers that it's the anniversary of a year passing since Aoba's arrival. Aoba is disappointed that he guessed it right so quickly, but then points out that he could only know if he remembered it too, with Mink immediately changing the topic.