"Help Eliwood? Sounds like a convenient excuse for more violence."
Upon Florina's doubts of becoming a pegasus knight, Sain steps in to convince her that she should continue, since Lyn's group with the inclusion of Wil is basically a freelance mercenary group that she needs to train with. Cue Wil being confused about what Sain said.
Wil: Wait, did you just include me?
Admittedly, even the tactician gets a few good ones to certain characters.
Serra: What I'm getting at is... I'm thinking of healing [Erk] for free. I know, I'm generous to a fault... Hm? Why are you giving me that look?
Chapter 6 of Lyn's story has an interesting one. Rath berates you if you don't move him to the trigger after Matthew unlocks the door.
Rath: Do you see a trigger there? I didn't think so.
Deciding whether to take Nils and Ninian into Lyndis's Legion:
Lyn: What do you think, Kent?
Kent: I think leaving them here will make you more worried than taking them with us.
Lyn: And what do you think, Sain? ...wait, never mind.
When the resident Large Ham Wallace urges you to use his crest.
Among the credits for Lyn's story, Sain, Florina, Serra, and Wallace are probably the most notable for potential humor.
Speaking of Wallace, his tendency of getting lost can become even funnier in hindsight no matter which version of Four Fanged Offense you get. If you get Lloyd's map (in which Wallace returns), Wallace's ending will talk about how he got so lost he somehow ended up in Ilia. In Linus's map, Wallace doesn't even show up and is never referenced again, so the last thing he does in the game is get lost either way.
Hector's comments about Matthew.
Man, why do I get stuck with all the lame henchmen?
Also, his comments about Matthew and Serra in Chapter 12, along with them each insisting he was talking about the other one.
Eliwood: Whose snoring was it that shook the rafters in numbers class?
Hector: Ah, good point.
Eliwood sort of gets him back in his B Support.
Hector teasing Eliwood about his potential crush on Lyn in the first side quest.
Then later, blundering around when confronting Merlinus.
Eliwood: Hector, your manners are terrible.
Erk and Serra's reunion. Erk isn't so happy about it, while Serra flips what he says around.
Erk: Oh, Serra... you're the last person I wanted to see.
Serra: Oh, that's so sweet! You wanted to see me again!
In Chapter 15, you have the option of bringing certain characters to talk to Lyn on the battlefield. Some highlights include Matthew blowing his cover, again, and Hector running off to fight and prompting Lyn to call him back.
Serra and Lucius' supports.
C Support, Serra gets bitchy at Lucius because she thinks he's a girl. Lucius confesses to Serra that he's a monk therefore a guy. Priceless.
B Support, she has a full blown crush over him, and Lucius is oblivious to it.
Guy and Matthew's C Support. It consists of Matthew dragging out the favor as long as he can. Guy isn't amused.
In a later support, Matthew sneaks into Guy's tent to ambush him in his sleep after Guy challenges him to a duel.
In the A Support Guy goes after Matthew in the same fashion to earn his payback. It does not end well for poor Guy. Not only Matthew realizes as he gives Guy a pretty bad bump on his head. The way Matthew starts the conversation is what sells it.
Chapter 17: after pulling up the Dory, we find that it's Ninian in the ship. Dart, not knowing how to help her out, asks for Lyn's help. In the most awkward way possible. Hector doesn't miss the chance for a comment.
Fargus calling Dart an idiot before he joins. Then, Dart later calls Fargus's crew a "suicide squad," possibly in part to get back at him.
Hector and Lyn's argument in the Chapter 18 sidequest. The argument? Figuring out who's making more noise; Hector's armor or Lyn's yelling.
Hector, the red oni to many characters in the team, being nice at any point in time.
Chapter 20, we have Hector worrying about what Lord Uther will say to him when he finds out he's traveling with Eliwood and Lyn. Cue some rather funny Mood Whiplash when Eliwood (who had earlier been mourning over his father) suddenly starts teasing Hector about it.
Chapter 21 has Lyn commenting on how unconventional the Ostian family is when Lord Uther tries to make his way to the castle. Hector, being Lord Uther's brother, didn't like that.
Eliwood's confusion when trying to talk to Hawkeye and Lord Pent.
If Hector goes to talk to recruit in the chapter Living Legend this will lead to a rather humorous dialog:
Hector: Ahhhh... Shadow... Wait. Shadow?!
*turns around to see Hawekeye right behind him*
Chapter 22, if Hawkeye makes a trip to the house, he'll have a special conversation with a girl named Fae. She'll go on to criticize Hawkeye for always responding with his trademark catchphrase. What happens next?
Hawkeye: Is that- ...sorry.
After reaching Dread Isle, the fortune teller starts getting cranky for dragging her to scary places starting at Chapter 17. At one point, she upright quits to let Nils take over her job.
Priscilla and Heath's supports.
C Support, Heath introduces himself and his wyvern Hyperion, who seems to be feeling unwell. Consulting Priscilla, she admits to overhearing Merlinus complain about something raiding their supplies...
Heath: ...I don't suppose we could keep this between us?
Saul and Dorothy's C support features this gem:
Saul: Of course. However, while I was doing my job, a young maiden was being harassed by a very rude man.
Dorothy: You mean yourself?
Saul: Do I not have any trust at all? Anyway, I drove off the man and rescued the maiden. I must admit, I acted exactly like a holy man ought to behave.
Dorothy: Really? You're not exactly very strong. How did you do it?
Saul: I went to the man and clung to him, crying, 'I thought we loved each other, and now you are rejecting me?'
Saul: The man fled with haste. However, the maiden was also gone when I looked back...