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 Genjiin 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.