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.
After Noire fakes amnesia, Neptune wants her to join the team.
IF: Neptune, you found her, so you better take responsibility for her.
Neptune: Alrighty! I'll feed her, potty train her, take her for walks, and get her spayed until she remembers something!