The eating contest at the start of the episode. Haruto and Shoko were picked by their respective clubs to compete, and whoever won would choose who got to use the grounds. Some transfer students are disgusted by it, but meanwhile all of Haruto and Shoko's friends are hamming it up cheering for them. Shoko wins.
When Shoko says Haruto has a tendency to get cold feet he replies "Says the girl in the weird t-shirt", at which Shoko looks around before pointing at Marie (who, for the record, is wearing a plain white and red t-shirt). Cue everybody pointing at Shoko.
In Episode 4 it's hard not to at least smirk when The ARUS Senator says: "Call me Moses, because I'm about to part a sea of students".
"Out of the way if you don't want lead poisoning!"
Later on, as they're sneaking into the building that Figaro and his men are using, Yusuke admits that he knew how to get in because it's the building that the girls always change in before the annual beauty contest. Shoko suddenly pauses, blushing, and this causes the air vent they were using to collapse. Shoko winds up landing on top of the guard who was watching Haruto.
Raizo and some other guys decide to make the most of their modules Teenage Wasteland state... by watching lots of porn in a theater.
In Episode 5, the Sakimori students produce a music video in order to help raise funds and get the word out that they're doing well to the rest of Jior who are currently under the strict rule of Dorssia.
In the video, there are at least two giant paintings of a scantily clad anime girl made by the school's resident Otaku. They also dress up in silly cosplay later on.
Raizo dropkicking a guy in a dinosaur costume.
A-Drei throwing his glove at the television in anger when he sees the video. Q-Vier is also present, and completely losing it.
This image◊ (warning for some strong language) makes it funnier—it pretty much sums up all reactions to the show itself.
In Episode 6, we've got Saki putting the moves on Takahi while in possession of Haruto's body. There's just something so wrong, and yet so amazingly hysterical about watching "Haruto" acting so smooth. When you think Haruto is about to kiss Takahi, he puts a pink Pocky in her mouth.
Watari crying when pictures of Haruto and Saki together are uploaded on the net by "Haruto".
When A-Drei jumps L-Elf in Episode 7, L-Elf immediately grabs the hapless Haruto and uses him as a human meat shield◊ against A-Drei's sniper rifle. This in itself wouldn't be all that funny if not for the context, in which Haruto is immortal and L-Elf is fully aware of that fact,
Before that in the same episode, L-Elf tried to make Shoko agree to his thoroughly written out plan of making New JIOR a military state. When Shoko refuses L-Elf activates the traps he set up in the school and declares he has now taken over. The only ones to oppose him are Saki and Raizo (who, by he way, climbed up to the home economics room in the third floor where they were, entering from the window) L-Elf admits he did not factor their opposition into his plan, but a few seconds later, we see Saki AND Raizo knocked out, with L-Elf commenting that he did not have to.
Despite the way her food looks everyone, even L-Elf, agrees that Shoko's cooking tastes good.
This is, in fact, a Shout-Out to Hitman. If that makes it even funnier or not is up to the viewers.
Valvrave 3 does, in fact, have 10 arms as the female Dorssian vice captain states the obvious in episode 9. Before that, she pointed out that the Karlstein Institute is a training facility for Dorssia's special agents and not spies. Although she dies quickly after.
The simple fact that as of episode nine, Haruto and L-Elf are officially roommates.
YMMV, but the return of Shoko's cartoon t-shirts during the "students training montage".
Raizo's explanation of why he named his Valvrave 'Nobu Lightning'.
Raizo: That 'Unit 03' shit is for pussies!
In episode 11:
Haruto: "This is insane, just how far can he predict things?"