The first time Deis is in a non-robotic body. The first thing she does? Kvetching about the body. The second thing? Putting Lina Inverse to shame in the Big Eater department and justifying it as offerings.
That whole "ship" thing was a giant Moment of Funny for Ursula. When the sailors first protest about a woman being on their ship, Kahn shows up out of nowhere, Ursula shoots him down, then says "Can I join now?"
And during the actual voyage Kahn attacks the ship and Ursula is up in arms because she thinks they are back.
Right near the beginning, Ryu and Nina are walking on a cliff when Nina slips and falls. Ryu, ever playing The Hero, jumps down to save her...then on the way down, sees her wings...and has an epic faceplant.
Scias's priceless reaction to what a Faerie Drop actually is.
Nina meeting Ryu, who happens to be naked due to just appearing. She turns around and awkwardly asks him to put some clothes on and Ryu just looks at her, then he looks down.
In the manga, Nina calls Cray "Nii-sama", which is a very formal and personal way of addressing your big brother, so when Ryu finds out that Nina and Cray aren't actually related, his response is "That explains why they don't look alike." with an image of the two in the background.
In the game, you have to fight Kahn to gain entry to Mardok's house. In the manga, Cray just hits him over the head with his club.
All of the omakes. In particular, Fou-Lu quoting Milkshakes in his Ye Olde English manner of speech.