One of the interesting pranks could be Naruto disguising as a clan elder and giving out really strange and comical orders. For example, he might tell the Uchiha clan to start wearing pink headbands for a week just to see their confused reactions.
He could also prank the Inuzuka clan by making them think that all their ninken have suddenly lost their sense of smell. Naruto could use some basic genjutsu to create this illusion, and watch as the Inuzuka try all sorts of things to fix the 'problem'.