Neptune and her friends beat up Black Heart for the something-th time in a row. Then this dialogue happens (this is paraphrased a bit):
Neptune: Ha! You can't beat us! We fight for justice!
IF: Yeah. Three on one. Such justice.
Early in Lastation, a story quest involves finding a child that has gotten lost somewhere. Compa then says something so unexpected in regards to something that has never been brought up before that it can't help but be funny (therefore, the joke isn't that funny if you're expecting it, but still.):
Neptune: What's this kid look like?
Compa: The mom said her/his body is just an NPC silhouette so she/he should be easy to spot.
Jade (a minor NPC) and his death at the hands of Magiquone/Arfoire is THIS.
Neptune: Oh, yep. Death flag triggered. I kinda guessed he was one of those gonna-die-NPCs when I met him. Is he okay?
Neptune: Oops. Well, that was for ruining the moment.
Using Neptune's ultimate attack, CPU Neptune, summons a ship that fires a giant laser onto the enemy. Said giant laser also consumes the entire land mass and looks like it's destroying it too. However, in the bottom-right of the screen there is a disclaimer of, "This is not actually happening."
The beginning of the game where Blanc refers to Vert as "Thunder Tits". This nickname has been kept in later releases, especially in Victory.
During the conversation between Neptune, Noire and Plutia when Neptune first goes to Planetune in the 80's, Neptune claims Noire has no friends. Both Noire and Plutia's reactions to this are priceless. Funnier is Neptune's reaction after she finds out Noire DOES have friends.
Anytime Iris Heart is on the screen. Anytime.
Special mention goes to her first scene, where she politely asks the villain present to wait while she torments her party members for a bit. After an... intense set of bargaining, she eventually thanks the villain for her patience. Said villain admits she just didn't want to have a yard of what was going on.
Pirachu called Arfoire "OBAHAN" and thus made her mad.
In English, the lines were more generic "old hag" insults that still spark her ire, but lack the same impact... until Pirachu tells Plutia Arfoire is only so cranky because she's menopausal.
This doubles as a Call Back to the first game when IF made a comment about menopause when Arfoire first appeared.
Plutia questions why you don't have to travel through a dungeon in order to reach another nation in Neptune's world.
Neptune: Yeah, we retconned that.
Shortly thereafter, they comment that things would be so much easier if Noire built a road connecting the nations directly, only to hear Histoire yelling that they should do something about it... and then remember Histoire is nowhere near them right now. They were so lazy their own subconscious yelled at them to get something done. In unison.
Nep: (comparing Blanc and Plutia) And when it comes to HDD, yours is so much crazier.
When Noire, Neptune, and Blanc see Plutia holding baby IF, Compa, and Peashy, they all immediately assume she was pregnant during their absence and the children belong to her. Their overreactions are hilarious, right down to Neptune starting to recite the numerals of pi.
Nepgear gains the “Emo” Affinity! Neptune: The game system popped some kind of window up! What’s an "Emo Affinity"? Glad you asked. By worrying about her lack of personality, Nepgear acquired a "Learning Ability." Depending on the situation she finds herself in, she may learn various other unhelpful things. That is to say, these don’t affect the game in any way. Neptune: Whoa, a self-aware tutorial window responded to me!
When Yellow Heart first appears, both Vert and Blanc agree to take her out, so Vert can have the largest chest among the CPUs again.
"I AM GOING TO LOWEE. THEY WILL HEAR ME COMPLAIN DIRECTLY. IN LOWEE."
In case you're wondering, Noire complains so much until Plutia gets fed up, transform into Iris Heart and teach her a lesson, resulting breaking Noire. This continues even in the Basilicom, where Noire still sounds like a Broken Record, while Plutia is rather... satisfied.
After Neptune comes back from Leanbox and Nepgear is depressed because her sister left her behind, Neptune tries to make her feel better by saying she loves her. Also remember that IF and Peashy are still babies at this point.
Neptune: Nepgear! I, Neptune, your big sister... looooooves you! Nepgear: ...Huh? Plutia: Oh, my! Incestual confessions! (*Neptune and Nepgear continue to confess their love to each other*) IF: ...Dis is hawt. Peashy: Ooh, lovey-dovey sistahs.