Dart telling Lavitz that they ought to take a nap because rest is good for the skin and every young lady ought to know that.
In fact, all the various suggestions you can give Lavitz when visiting his house.
Kasier telling Shana he does not mind how bad her cooking gets cause they can always drown it out with salt.
Mappi and his pals, when they face you for the first time.
There's a very funny but optional cutscene that happens after you helped the little kid and his mother to reach the city on the island in Illisa Bay during act two. If you visit him later in the clinic he'll tell you about his wish to become an adventurer like Dart. Depending on your answer, a funny event with Meru/Rose/Shana will happen.
Near the end of act 2, you have to look for your friends in Zior's castle. You stumble into Meru and Haschel as they're being kicked out of the kitchen, and you can have the chance of supporting their idea.
A mininto in Lohan offers to Dart a "Special Ticket" with the front printed on the back and the back printed on the front. Then when Dart asks him what's the actual difference from a normal one, he realized that he has been tricked and goes apeshit.
During the tournament in Lohan, if Dart loses the first match, his opponent will attempt to kill him and thus be disqualified. After this happens, Shana will say that she wanted to shoot the guy with her bow and Rose will remark that her opinion of Shana has improved.
A bit of Mood Whiplash, but when a Big Damn Heroes moment is pulled right before the final battle. Despite being a Cutscene, it uses the battle engine, angles, plays the light-hearted standard boss battle theme, and the EXP distribution screen even shows up afterwards. Given that this followed a rather serious moment, but it's hard to tell if it was intended to be funny or not.
Meru puts her hands over Dart's eyes and says "Guess who". Just looking at the options are just plain humorous, imagining how stupid (or sarcastic) Dart would have to be to imagine that it's Rose, Haschel, or Kongol.
During Dart's and Shana's reunion (after he and Rose fell overboard), their touching moment is interrupted by Meru, Haschel, and Albert listening at the door.
During the aftermath of the attack on Hoax, Shana ask who Rose is to Dart. If you say she's an important person to you, Rose asks if you're trying to seduce her.
Mr. Magi's botched attempts to perform magic are first met with wariness but it quickly turns to boredom as his spells fail. The one that finally succeeds is his Cerberus transformation... which turns him into a normal dog.