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In the anime, the members of the Future Gadget lab have already used the Phone Microwave (Name Subject To Change) to gel-ify bananas so it's not the first time they've done it when we see them do it on-screen. However, the Visual Novel shows us the very first time Okabe & Daru manage to time-warp a banana. Their reaction to this is a wonder worth seeing.
"Anata no banana pyun pyun da ne!" Your banana is so soft and squishy, but yours truly Mayushii!
Any time Okabe goes off in weird tangents of thought, leaving everyone bewildered.
EVERY time Okabe talks to his Imaginary Friend on his phone, to the point that he has to come up with Blatant Lies as to how his phone magically turns off when anyone besides him touches it when Kurisu grabs his phone and sees that it's off. While many of Okabe's paranoid and/or nonsensical rantings turn out to have some measure of truth to them, this is the one aspect of him that is purely fictional.
There's one moment when he calls Kurisu using his self-appointed name for her, "Christina," except he draws it all out so long it sounds like he's trying to sing opera.
This talk from episode 3:
Daru: What do you want the text message to say?
Okabe: How about "Christina is a pervert."
Kurisu: Don't go pushing your luck jerkwad.
Daru: How about I just split the difference: "Okarin is a pervert."
Kurisu: Atta boy! Good thinking!
Daru: Firing torpedoes, captain!
Okabe & Makise getting into an argument over which of them is the bigger pervert. "Hentai tensai shoujo yo!"
Any time Daru keenly takes notice of a Double Entendre, since the viewers usually notice them at the same time.
Also, any time Daru compares what's happening in-universe to a LN or an anime, considering the show's source material.
Any time Moeka talks about how much FB means to her because to a lot of people interpret it as "Facebook"
While serving a microwaved banana; "Enjoy, I demand it!".
Kurisu's tsundere moments. For example, this little gem in episode 12.
Kurisu: "I-I'm not... I'm not grateful to you. I'm just being polite..."
Okabe: What kind of tsundere is that?
Okabe discovers, in one world line after he sends a D-mail, , that Ruka is now actually a girl instead of a guy wanting to be one.
...the hard way... Episode 14:
"Right now, What you want most is your own personal fork."...look at Kurisu's reaction.
: "Screw you future me!"
The Gratuitous English makes if even funnier. "My fork" and "my spoon" indeed...
Apparently "my fork" and "my spoon" was at some point 2chan slang for "lover" and "friend", respectively. No wonder Kurisu was so pissed with herself.
Okabe's reveal of his @channel handle, "Hououin Kyouma", which everybody already knew.
Okabe's attempt to communicate with a foreign looking person.
Okabe: Word to your mother!
Episode 18: Kurisu recognizing that Okabe is a virgin.
Episode 23: Okabe describing his future self as "an otaku who read too many bad light novels". This is sadly lost in the dub.
Episode 25: The return of Gratuitous English Okabe, only this time he tries on American airport security. It goes slightly less well.
Security Guard (In English): "What's your purpose here?"
Okabe (in Japanese)
: "I guess I have no choice..." (switches to English) "I am mad scientist! United States! Chaooooossss! And invade!
*begins to laugh maniacally*
IT'S A MOTEL!!! What does Moeka want? "MACADAMIA NUTS MACADAMIA NUTS MACADAMIA NUTS MACADAMIA NUTS... anything but"
Kurisu in the cat maid outfit.
If you're a Los Angeles native, it's pretty amusing to see familiar places in this episode. The details of the Staples Center, LAX, and the LA Convention Center are spot on.