Lute attacking Knoll twice after he points out he's been stalking her for a while (in their C Support). Not only does Knoll dodge all the blows and escape from her, but she comments he's dangerous just because nobody has ever dodged her blows (at least story-wise).
Lute's supports with Artur are a riot. Key moments include their B support, where Lute had tried to help Artur overcome his fear of spiders by covering him in them while he slept, and their A support, where Lute doesn't know how to react to Artur's confession of love as none of her textbooks describe what being in love is like.
When Joshua attempts to hit on Natasha—a nun, with actual vows of chastity implied—and she is so distracted that she doesn't even notice.
L'Arachel's supports with Ephraim are all hilarious, especially when his slightly unclothed body completely breaks her delicate sensibilities.
In Chapter 10, on Eirika's path, Innes fires the crew of mercenaries he hired to convince them to abandon him and save their own lives when they're outnumbered and under siege from an enemy army, but they refuse. The mercenary boss refuses and then tries to get his female second-in-command to flee, who cuts in:
Tethys: Would the two of you kindly stop acting like such... men? And you! You've already fired us. You can't order us to leave now.
His supports with L'Arachel are among the biggest proofs. You know she's the Tsundere of the game... and yet she brings the Tsundere out of Innes and they pretty much try out-tsunning each other. With manners.
Garcia: That did not go as well as I had hoped. Dozla: Well, that's not entirely true, is it. Garcia: It would have helped if you hadn't whacked me in the head with the staff. Dozla: I didn't mean to hit you! You just got in the way when I was...conjuring. Garcia: I still have a lump on my head. Dozla: I feel badly about it, all right? Besides, I think you're forgetting that I also healed you with that staff! Garcia: No, you didn't! You burned my beard clear off! Dozla: Oh, yes. That's right. I'm sorry.
Having Ross promote to a fighter or a pirate will solicit a couple of giggles. The kid pulls out pounds of muscle from the fucking ether, and the change between his journeyman class and both of his promotions is something you'd expect from Pokemon.
Ephraim's B Support with Tana. Tana tried to make Ephraim about how they first met... but all Ephraim could remember was his 'competition' with Innes. Tana is justifiably pissed off for being forgotten and ignored like that.
On Ephraim's route, having Joshua fight Caellach has them talk about their time as mercenaries and is somewhat less emotionally charged than on Eirika's route, if you have Colm as a Rogue or Rennac steal the Hoplon guard from him and then attack him with Joshua you can one shot him with a critical hit, Right after he claimed that he was way out of Joshua's league.
Joshua getting utterly confused and frustrated during his supports with L'Arachel, as he cheats and cheats and cheats and yet somehow she still wins.