The Prehistory chapter has too many to count, but the highlights are:
After the pitfall, Pogo jumps over the whole, then looks to Gori and expect him to do the same thing. Instead, he pulls a classic comedy trope by walking back the way the duo came from and then reappearing on the opposite side. Pogo makes no surprise or reaction to this, and this is done every time you jump over the same pit hole.
When resting at a cave, Gori lets out a big gas cloud. Pogo and Bel just watch it silently as it goes in a circle... and floats over their campfire. Explosion ensues.
In Sundown's chapter, you are warned from the daughter not to go into her dresser. You can only do so when she's out setting a trap you gave her. When she comes back you can give her the nighties you found in her dresser... which prompts her to slap the cowboy.
In Akira's chapter, there's a bit of perverse humor centered around Takeo. First, whenever Akira goes to the can, Watanabe comes in to give him a certain item, but keeps screwing up. First it was his own pair boxers. Then the Director's. Then Takeo's Jeans, then stockings... then Takeo's Punch, which she personally delivers when she finds out what Akira's been doing (and Akira shares the reward to Watanabe for screwing up). Going into the bathroom one time allows Watanabe giving you the desired item; Takeo's Panties.
Also, whenever fighting Crusaders, Akira makes use of Teleport, which is like Fleeing but sometimes sending him back to the Orphanage. At one point he either ends up in the kitchen sink or the bath tub. One instance might even have him appear in the tub while Takeo is washing herself naked.