Well, it could be that Naruto pranks the clans to test their reactions and sense of humor. Maybe he uses simple tricks like fake summons or changing the appearance of clan symbols to see how they respond.
Sasuke could be one of the main characters. He might be initially annoyed by Naruto's pranks but then end up getting involved in some way, either trying to stop Naruto or joining in on the fun.
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.
One of the funniest pranks could be that the Kyuubi makes Naruto's clones start singing cheesy pop songs instead of following his commands. Naruto often uses his clones in battles and for various tasks. So when he sends them to attack an enemy, they all start singing and dancing instead. This would not only be a shock to Naruto but also to his opponents. Another great prank would be the Kyuubi making Naruto's body move in the opposite direction of what he wants. So when he tries to jump forward, he jumps backward instead, leading to all sorts of comical situations.
Well, the Celestialsapien could have a special connection with the Uchiha clan. Since the Uchiha have powerful Sharingan abilities, the Celestialsapien might be interested in studying it or even enhancing it for some of the clan members. This could lead to a new kind of power-up for the Uchiha in the fanfic.
One of the pranks Naruto might do is to mess with the Anbu's communication system. He could use his knowledge of chakra and some basic electronics (if we assume some modern - like elements in the fanfiction) to scramble their signals. This would make it difficult for them to coordinate with each other, and they'd be running around trying to figure out what's wrong while Naruto watches from a hiding place, having a great laugh.
He might get paid in ryo. Some rich clans or individuals who want to see the chaos might offer him a sum of ryo for each successful prank he pulls on a particular clan.
Naruto could enlist the help of his friends like Shikamaru. Shikamaru could come up with a really elaborate plan. For example, they could set up a fake mission where Ibiki thinks he's in charge, but it's all just a setup for a series of pranks. They could have actors pretending to be enemy ninjas who act really silly instead of being threatening. And Naruto could keep popping up in unexpected places during this 'mission' to further annoy Ibiki.
He might replace Sasuke's kunai with candy - shaped ones. It would be really funny when Sasuke tries to use them in a fight or training. Another prank could be that Naruto hides Sasuke's training gear and replaces it with a bunch of candies.
In a Naruto pranks Hyuuga fanfiction, Naruto might use his typical mischievous tactics. For example, he could use his shadow clone jutsu to create chaos around the Hyuuga compound. Maybe he'd make clones that pretend to be important visitors and then act all silly to embarrass the Hyuuga. It would be a really funny scenario as the serious Hyuuga clan tries to deal with Naruto's antics.