It comes after the terrible deaths of hundreds of people in chapter 6, but Nagate staring at and holding a flapping fish is pretty funny, since it almost seems as if he's considering eating it. "Leave the fish, Tanikaze."
The Bathyspere scene, or rather the lead-up to it, is harem comedy at its finest.
Any single time Izana pouts out of jealousy when Nagate doesn't notice her, an expression commonly referred to as 'the Izanaface◊'.
A pretty noteworthy scene in chapter 37 is when Izana and Nagate are simply having a quiet moment in the former's house, talking and eating food. Suddenly, Izana trips while carrying a plate holding an onigiri. As the action slows down, we see Nagate quickly look at Izana and then the onigiri, as if deciding which to catch. His solution? Save Izana, who catches the onigiri. Then it turns out Nagate has his hand on Izana's chest, causing some awkwardness. Then Tsumugi's tentacle head bursts in unannounced into the house, causing them to scream. The whole sequence is hilarious.
Tsumugi (or rather, her tentacle head) living in Tanikaze's house.
The anime includes a scene in which Izuna explains to Nagate that their skinsuits contain automatic catheters. Cut to the Hanoka sisters suiting up in their locker room in the midst of a simultaneous Luminescent Blush, back to Nagate looking extraordinarily uncomfortable as his suit goes to work, and Izuna...is just fine.