From chapter 4 of Unreal Society, Shuhei says that Lloyd seems like the type to go barging into political estates and maiming its higher officials to rescue a friend in need and says it sounds familiar, referring to Ichigo, prompting the teen to snap at him.
Raine exploding on Ichigo after he suggests blasting open the door to the Tower of Mana in ch 8 of Unreal Society
Raine tugging on Ichigo's ear for attempting to suggest that he and the others could rough up the royal guard if they gave them any trouble in ch 10 of Unreal Society
Ichigo comparing Zelos to Kon when he first meets him.
Sheena saying that Zelos has about the same Charisma as a warthog.
Rukia's response when Genis tells her in chapter 12 of Unreal Society she's the most mature of the group.
Rukia: (thinking) I think a twelve-year old just massaged my ego.
In Chapter 19 of Unreal SocietyRaine is picked to cook for the Gnomlette, an already humorous bit in the actual game, but it's added onto when Rangiku volunteers to have some, likes it and then Genis tries some only to require first aid be cast on him.
Chapter 20 of Unreal Society when Ichigo and Lloyd are training and both attempt to stay out a little longer only for their stomach's to demand food.
Rukia: It's a type of Hybrid Plant Monster composed of several kinds of cacti, Venus flytraps, roses and thorn bushes. It's an aggressive, living animated plant monster. It enjoys wrapping it's prey in it's numerous tentacles and binding them tightly before opening its large mouth and swallowing them whole.
Ichigo: That's it when I get home I'm swearing off vegetables for a week.
Lloyd trying to have a full length conversation with Chad.
Tenebrae: It seems you are berry good at attracting vine young ladies.
After being called on that very pun
Tenebrae: Hmph, it seems my sense of humor is juice too refined for your tastes I guess.
This when Emil is ice fishing for jellyfish:
Emil: You think we should change bait?
Tenebrae: Perhaps we should get some peanut butter.
Emil: Peanut butter?
Tenebrae: You know, peanut butter for the jellyfish *laughs*
Raine exploding on Ichigo after Tenebrae reveals what Ichigo did to the Asgard Ruins, despite his attempts to keep it a secret from her.
When the path behind Celsius' altar forks, it's very obvious which one has the core and we get this gem from Ichigo:
Ichigo: Man the only way the direction to Glacies' chamber could be more obvious is if there was a big flashing neon sign that said "Core here, graverobbers welcome".
Presea's mention of the curse to anyone who opens the Iron Maiden before the proper date is already one of the funniest moments in Tales of Symphonia: Dawn of the New World, but in Return of the Samurai the funny doesn't stop at Prsea getting away with her lie.
Ichigo: I can't believe you said all of that with a straight face.
Presea tying Kon to the shaft of her axe after Ichigo tells her to treat him like Zelos. The action is not only funny by itself, but it begs the question of some things Presea may wish to do to the actual Tethe'alla chosen.
The omakes at the end of some chapters. They really are hit or miss.
Parts of Pesche's narration in ch 17 of Blades of Destiny have their moments.
Presea speaking in a Creepy Monotone to Kuchinawa and his assassin's guild about how being killed by a Soul Reaper would feel to persuade them to fight for Aselia for a reasonable price. It's funny, cause it's Presea.