Ōkamiden/Funny

Kagu doesn't want anyone to know of her powers. When Chibi sees her using them, she orders him to not tell anyone, and demonstrates what will happen to him if he does... she will shake him violently.
- She does the same thing to a stagehand shortly afterward.
After saving the theater, one actor will be in front of the toilet and complain about how long the person inside is taking. Visit even later, and he will soil himself when you talk to him again.
This gem from Gen, upon being given a stone slab with an image of a flying saucer on it

Ooh, another dubious contraption! I must work on it before I do anything else!

Chibi decides to handle computers by slamming on the keyboard repeatedly all while happily wagging his tail.
"The password guy came by. He said, 'Now, everyone will know THERE'S A BIG DEMON FACE IN THE WAY!!!!'"
The fact that we learn that Benkei's quest to find the 'Living Sword' was the result of an old sailor essentially trolling him.
During the chase sequence with Genji, during one of the moments when he's freaking out, he suddenly pops up at the front of the screen and makes a heart at the player, before running off. Or heck, just Genji in general.
Take Kagu into Mr. Chic's shop after removing the curse. Examine the front counter, which for some reason has a statue where the cashier should be. Her immediate reaction:

He turned his wife into a tanuki!!

After you (once again) restore all the cherry trees in the Commoner's Quarter of Sei-an City to full bloom, Mr. Blossom will tell you that, "This is either the work of a higher power or that big dog from that one time!"
Kuni's introduction when he falls flat on his face after jumping off a roof.
The Running Gag of Chibi's nicknames never fails to be funny. It's just the expression that sells the joke. Then even after people know his real name, meet up with other people that different nicknames they still insist on calling him Squidy and Pork Chop.