Shinji gets a text from a classmate asking if he's Unit 1's pilot. As the action figures weight in, three of them suggest lying and the Space Marine says "lies do not please the Emperor!". The Space Marine wins, Shinji is surrounded by hostile stares, and the other three dogpile him. They tie him up and gag him. Imagine all this happening over Shinji's head.
'If the boy is a Messiah, then that would makes Gendo Ikari...? Hell no.'
"... actually, I would rather accept the boy being born of virgin birth than contemplate that someone as intelligent and attractive as Yui Ikari would even touch a slimeball like Gendo."
"The Emperor's soap" springs immediately to mind. Perhaps surprisingly, these moments can occur even in the middle of pitched battles ("HALT! Hammerzeit!")
In Chapter 41, the fact that one of the Mass-Production Evangelions is at one point described as having an "I has a sad" expression.
Chapter 21: "... did you actually say 'Schwiiing!' as you turned your chair around?" Gendo merely entered into a profound silence.
In Chapter 38: Half the chapter is spent detailing how one man heroically manages to take down a gigantic robotic dinosaur. The other Tyrant King?
Asuka Langley-Sohryu punted a nearby Tyrant King into the horizon. Though twice as large as a real Tyrannosaurus Rex, they were perfectly sized for kicking.
In the last few chapters, Kaworu's running internal monologue as he tries to figure out what Shinji is planning next, including such gems as this: 'What? He can't have run out of power yet.' The Evangelion remained on its feet, the glow in its eyes a steady bright orange. 'Oh, shi-. Am I standing on an N2 Mine?' In fact, Shinji is unconscious.
And our beloved noncanon berserker... "FEEL THE -POWER- OF MY OPPOSABLE THUMBS, -BITCHES-!"
The dialog with the Space Marine on the topic of chainswords.
'Be blessed in the name of the Emperor.' said the Space Marine. 'Be blessed by the anger of the machine spirit. May your bite bring His rage, may your roar echo His wrath.' "Um... I'm going to use it mostly to chop wood." 'Chop wood in righteous -anger-, then. In the Emperor's name, may they be -torn- into pieces suitable for re-assembly! Let them come together in praise of his Will!'
"There were scale models of the Evangelions, pilot profiles, books, toys, and assorted merchandise. The Whack-A-Gendo game was (un)surprisingly popular."
The Emperor's soap. Shinji finding a chainsaw. Da Boyz and their behaviour in the presense of Da Boss. The Ship-to-Ship Combat between the students. Rei, Orky superhero ("Waaagh"). "Damn you Ikari!". The Eldar Farseer's... propositions. Kensuke's ever-growing devotion to the Machine Spirit. Ritsuko's ever-worsening hysteria as Shinji makes balloon animals out of physics. Being fired upon by fireworks. Like with Crowning Moments Of Awesome, Shinji And Warhammer 40 K merely requires a page to be picked at random.
We can't forget the Farseer handing out Dope Slaps while the Marine moans about Leman Russ, "Gendo, you're an asshole!", and the Farseer and Warboss collaborating on a plan to kick Gendo in the teeth. This is in the first two chapter and prologue.
Farseer: "Remember, plan sequentially. Kick him in the shin, first, and when he lifts his leg to rub it, you may punch him in the genitals. THEN when he's kneeling is WHEN you may kick him in the teeth."
The Omake in Chapter 20. Especially where Shinji's mother is involved.
Yui: Absence makes the heart grow fonder, and now he is even more attached to his girls; and vice versa. He has gained talents, decisiveness... endurance! My boy is irresistible! [dances with fans akimbo] Heirs! Grandbabies! By the score! Ohohohohohohoh!
Random NERV Staff: Aida's gone berserk! Run for your lives!
Suddenly, NAGISA INTERRUPT.
In chapter 5, Rika Izuna started making interviews in an attempt of riling the people against Shinji for demolishing half the city in the battle against the Fourth Angel. The first attempt offers us this gem:
Rika: "But sir, aren't you concerned that you won't have work the next morning?"
Interviewee: "... I'm a construction worker."
In chapter 16, Rei and Asuka have to sleep in the same room. Hilarity Ensues.
Asuka: "This is the unbreakable wall of Jericho! You -will not -cross it!"
Rei: "That wall... was broken."
Asuka: "Fine! An even bigger wall! The Great Wall!"