- Too many of the conversations during and the results of synthesis throughout the whole game. Some notable examples are Croix's umbrella spear that Cynthia calls "their child," nearly all of Luca's Cordon Bleugh Chef creations, Cloche somehow creating a bomb when trying to make a rubber duckie, and Spica being The Gadfly to Jacqli (and being the only one able to get away with it).
- Several of the character animations during synthesis count too: Cloche drawing up plans and somehow drawing a picture of a cat, Luca trying to hammer nails into a crate with all of them being crooked and of course smacking herself, to Jacqli waving a sword around that slips from her grasp and embeds itself into the wall (even with her head facing away from the viewer, you can still see her Oh, Crap! face).
- Despite Jacqli in her robot being That One Boss in Luca's route, she gets a moment when she leaves Dr. Laude behind and he has to scramble along, chasing after her.
- Level 3 Infelsphere. Put simply, it's takes the Love Triangle and turns up the romantic-comedy elements Up to Eleven.
- Alfman's lolipop gun.
- In a bit of a Call-Back to the first game, Jacqli as the third Reyvateil who joins the party will occasionally stumble when unleashing her Song Magic. She will quickly try to regain her balance, frantically look around to make sure no one saw, and then get back into formation in a pure "I Meant to Do That" manner.
- Amarie and Reisha's serious conversation at the start of Phase 3 repeatedly interrupted with Reisha's insistence that Amarie refer to her as "onee-san" rather than "oba-san" in Japanese.
- Cloche insists to Sasha that she is not the Holy Maiden after the latter realizes that she is and starts treating her formally rather than as her "Sis Clo." In order to help Cloche save face and because she insists, Sasha lists why Cloche couldn't possibly be the Holy Maiden: the perfect Holy Maiden wouldn't be so short-tempered, such a lousy cook, or ever come to a run-down shop like hers.Croix: Um... Lady Cloche?
Cloche: Please, stay quiet... I really want to cry now...
- After Cloche "takes Targana's life," she recruits him as her personal servant and immediately puts him to work in establishing the new Maiden Government while she continues the adventure with the party. His reaction is basically You Have Got to Be Kidding Me!
- Frelia's Binary Field story is full of them:
- Cloche's new costume from the story being a giant penguin suit. She pretends to be completely unamused during her talk topic about it, but she does a poor job in hiding the fact she absolutely loves it.
- How does Jacqli defeat Cloche in Episode 2? Attacking her with a Song that looks exactly like one of Luca's early recipes when synthesizing at Skycat's place.
- Skycat giving Jacqli a verbal warning that it's inappropriate behavior for workers at a maid cafe to blow up their customers.
- Shurelia breaking character to get mad at Jacqli for re-writing the story in the middle of it. Even better is that anyone who has played the first game knows that Jacqli is just getting a little revenge for Shurelia and Lyner doing the same thing to her, and unlocks a very powerful Song in the process.
- The fact that Aurica ends up playing the Syndicate Boss and equips her Don Leon costume as Powered Armor.
- Upon her defeat, Aurica calls Misha and Shurelia for help. Reisha defeated Misha while Jacqli didn't even have to beat Shurelia as Jacqli lets everyone know that Shurelia's No Sense of Direction affects her even in the Binary Field and she was too lost- two floors below- to arrive in time.
- Once it's all over, Luca and Cloche have a talk topic with each other where they complain about the terrible roles they got.
Funny / Ar tonelico II: Melody of Metafalica