The fact that the Updated Re Release shows Lynx flashing a shit-eating grin in the group shot. You'd forget he's a bad guy (unless we're meant to believe it's Serge in Lynx's body while Serge still shows up in the same group photo).
There's a part in the beginning in which, after enough persistent tries, the "barrel" you try to search through keeps on insisting it's "Just a barrel". Do it enough tries and it gets fed up with your persisting nagging and gives you what it was carrying after searching it four times.
No answer... It's just a "barrel"...
(when done the fourth and final time) Whaddaya want, already!? I said i'm just a "barrel!" Tch... Fine! Just take it, man! HERE! (Serge found Uplift in the barrel.)
Who could forget this dialogue from Kid when you meet her in Termina after recruiting Leena and staying at the inn?
Or the bit in the Shadow Forest where Nikki asks if you want to hear him sing, and all three options you can choose from are ways to tell him no.
In one of the battles with Solt and Peppor the former does something so stupid that for the rest of the battle Peppor does nothing but attack him. What had he done? HE WASTED A BLACKHOLE ELEMENT, which could not only instantly kill Serge, but also the entire party.
Luccia tells you not to release Pip... Right after you were already given the option of setting him free, and most likely did so.
If you choose to save Kid when she is poisoned, and reach the part where Korcha proposes to Kid (already a CMOF in itself), Serge can choose to encourage or discourage Kid to accept. No matter the choice, Kid will kick Serge in the groin.
The fact that the dwarves have an attack called "Hi-Ho Chorus" is absolutely hilarious. You are almost guaranteed to be laughing when it first goes off, even as it knocks your party flat on its ass.
Upon meeting Norris for the first time and explaining that "this is not Lynx; he has the body of Lynx, but his soul is Serge's":
Any time you meet Harle or she's in your party, though both her first meeting with Kid in Viper Manor and their second one at Hermit's Hideaway (if you save Kid) are especially hilarious. Especially since Harle is essentially the Dragon Gods' copy of Schala, meaning she's bitch-slapping and fighting with herself over Serge.
The Sage of Marbule is a literal janitor on Home World's S.S. Zelbess, but while he's a excellent kind of janitor that can kick your ass if you use any offensive non-trap elements on him, you can, in fact, GAIN his high-powered elements for your own use via Trap elements. The kicker here? You can run away as much as you want so that you prep up various Trap elements for you to use to gain the Sage's high-powered elements without fear of him annihilating you so long as you prepare the right trap elements. Otherwise, as long as you don't use any offensive elements on him excluding proper trap elements, he turns into a rather easy boss and a very rewarding one as well due to the aforementioned method of farming highly-potent elements from him via the trap methods to your heart's desire.
Given many characters are available, some are Joke Character if only for their inherent hilarity. A bunny girl who attacks with a carrot? An extraterrestrial that can summon a Megazord?
You can make a playable character meet its Alternate Self, and sometimes it's hilarious: aside from the regular "why is there another me" for most, Miki asks why the mirror is answering, Orcha gets so shocked he starts questioning his shadow behind him...
Radius both funny and awesome: He tries smacking his other self with his cane and the other Radius blocks it with his own cane. They both stand down, and Radius commends his counterpart for keeping himself so sharp.
Even comparing the alternate lives of NPCs can provide some laughs. In Guldove there is a leonine demihuman working at the docks. One version of him is too worn out to work and has to sit down, causing the other (human) workers to mock him for being lazy. The other version? Doing the work of several of the dock crew without breaking a sweat, while it's one of the humans sitting down wearily while gasping in disbelief, "How does he do it?!"
Zappa’s meeting his alternate self is also worth noting. There’s no confusion, no astonishment, just a simple and immediate “finally, another blacksmith with skills comparable to my own!”
The new dishwasher in Another Viper Manor who's constantly being yelled at by Orcha or getting trapped in Luccia's cages? Yeah, that's Norris. He even laments that he should've chosen an easier job and disguise for his top-secret investigation.
The creators made an eventual joke. Grobyc's name in Russian: "Grobys" is soft, diminutive, sarcastic version of the word "coffin". Wonder why (Determinator, Made of Iron)
Beat the final boss with Poshul at the start of the game, and Kid takes over the world, establishing the Acacian Empire.
Beat the final boss after completing Dario's sidequest and Serge is reborn. Dark Serge/Lynx, Harle, and Kid go to Termina's bar for a long drinking session... Which is run by Luccia, Karsh, and Marcy. Much hilarity ensues, one of which being Dark Serge bitching on how he hijacked a body that isn't of legal drinking age, and Harle ordering heavily-sugared coffee. When they get the bill, they're dumbfounded at how much it costs, and are promptly introduced to the complaints department... Zoah.
Beat the game after Viper Manor and choosing not to save Kid results in a terribly harsh but hilarious bit where Serge is now working at Lisa's Element shop and she and Leena proceed to have a catty exchange of cruel insults, she and Kid have a shorter one, and then Korcha tries to romance Kid again only for her to sneak out behind his back and be replaced by his mother. Then Solt and Peppor assault Fort Dragonia...with Pierre whom they've hired based on his false hero cred. He pleads sickness from eating too much at Zappa's, asking them "not to run", then when they get to the top of the fort fakes sickness again (the same way he did when trying to break in Viper Manor's gates) so as to get out of being the one to open the doors. (When the Shaker brothers say they'll try "Rock Paper Scissors" again he immediately leaps up just fine...) After this the screen goes black with the message "The three of them were never seen again."
due to the aforementioned method of farming highly-potent elements from him via the trap methods to your heart's desire.