In the first game, Cielo gets out of confinement by throwing a cat at the guard.
It becomes Hilarious in Hindsight after the reveal that the cat is sentient, and might even be his leader from the future.
Cielo is pretty good at providing these.
Ya can't be reasonin' with god, bro! Maybe I should show him some jammin' Latin rhythm, oh yeah baby, dig it!
Cielo's reaction to when he sees Argilla dressing as Sera is priceless.
Cielo: Okay... Dis seriously won't work.
Gale: Why is that?
Cielo: Obviously! Sera isn't dis tall, her hair is way different and her arms ain't dat thick— *Smack* Oow.
Argilla: Well, excuse me.
Mick The Slug trying to escape, only to run into the Embryon before Heat repeats his line about tearing him apart.
Setting up for the repeated threat, Argilla prompts Serph by asking, "What was it Heat said, again?" Your options are: "I think it was something like..." (prompting Heat yourself) or "I don't remember." Pick the second one?
Heat (to Serph): You really suck. (to Mick) I'm gonna tear you apart, you fat freak!
Titania threatening Serph when revisiting Coordinate 136.
Titania: I'll ram this Sugar Key so far up your ass that it can watch me kick the crap out of you!
Cielo suggesting that Sera uses jammin' Latin rhythm to quell God's anger, complete with a little dance. Fred's facepalming in the background really makes it.
The look on Roland's face when he gets called "the clever one" by Argilla.
The mantra named Wikipedia
The Hip Hop / Hee Hoo Brothers. Full stop.
Some of the NPC dialogue has its moments. In the second game, a member of the Lokapala tells Serph not to look down on him, he went to college! One of Serph's possible responses is "Which Tribe is that?" and the guy thinks Serph is mocking him. This is a Call-Back to a minor conversation in the first game where an NPC remembers once going to a tribe called "School".
Speaking of which, there are many minor conversations with the party members and Non Player Characters if you revisit locations you've already completed at various points in the story, and several are hilarious. Such as the party being weirded-out by a random ex-Maribelle NPC who wants Serph to devour her, the "School Tribe" discussion, or this conversation after the first cutscene at the New Embryon Base.
Getting ambushed by a random encounter and being killed with weakness exploitation before you can even move? For the most part, not funny. Taking a Gaea Rage that does thousands of HP of damage from the Demi-Fiend at the start of his boss fight simply because you dare to have an elemental immunity? Hilarious.
There's a Jack Frost in the second game that asks you questions about the first game and the events of the one you're playing right now. At one point, he asks a question about Mick the Slug. One of the answers is "Fat Freak".
When leveling up in the sequel, sometimes party members will somehow produce items from their mouths to give to the leader. Gale's mouth is actually his entire head, and his reaction to his head splitting open to reveal an item that he doesn't remember eating is hilariously deadpan.
It's not outright stated, but Argilla probably vomits items from her mouths like the rest of the Tuners... except her mouths are on her breasts. One of her item quotes has her say that her chest is on fire, and then she 'produces' the item in front of the party leader. If it's Serph, the narration notes that he is happy for some reason. If it's Gale, the narration will say that he is unmoved.
In the sequel, one of the kids in the underground city can challenge the party leader to a shoot em up game. Gale's refusal quote cements his status as The Comically Serious.
Gale: You will fear my elite skills.
At the Very Definitely Final Dungeon, Sera and Serph merged into Seraph. Heat expresses annoyance that they became so close... but admits that they're cute.