Scias' priceless reaction to what a Faerie Drop actually is.
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 Funny Moments for Ursula. When the sailors first protest about a woman being on their ship, Kahn shows up out of nowhere. Ursula nonchalantly shoots him down, skipping a potential fight with him, to prove her strength to the captain, who finds the situation awkward.
"Well...that's not exactly what I had in mind..."
And during the actual voyage Kahn attacks the ship and Ursula is up in arms because she thinks they are back.
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.