Well, Harry could use a spell to make Voldemort's snake Nagini start speaking in rhymes. Imagine Voldemort trying to have a serious conversation with his snake, but all it does is spout nursery rhymes. It would be both funny and a great way to annoy Voldemort. Another idea is that Harry could use a charm to make Voldemort's dark mark itch uncontrollably. It would be a constant distraction for him, especially during important meetings or battles.
Harry could use the Marauder's Map to always know where Voldemort is and then set up little magical traps in his path. For example, a puddle that turns into a sticky mess when Voldemort steps in it.
Maybe Harry could use a transfiguration spell to turn all of the twins' clothes into something ridiculous, like bright pink tutus. Since they are always the ones playing pranks, it would be a great turn of events. He could do it when they are about to go to a big event at Hogwarts, like a Quidditch match or a school dance.
One creative prank could be that Harry uses magic to make Umbridge's quills write only nonsense whenever she tries to write a decree. Another could be that he enchants her office so that every time she sits in her chair, it makes a loud and embarrassing noise, like a donkey braying. And he could also charm her teacup to refill with a really bitter-tasting potion instead of tea.
In the 'Harry Potter Pranks Everyone' fanfiction, there could be some hilarious pranks. For example, a student might use a charm to make the Great Hall's ceiling show embarrassing memories of the teachers. Another prank could be to magically swap everyone's voices, so that when they talk, it comes out as someone else's voice. There could also be a prank where the Hogwarts Express gets diverted to a completely different location, and the students end up in a strange magical place full of odd creatures and unexpected challenges.
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.
One possible prank could be that Harry and Luna use magic to make the Order members' shoes squeak uncontrollably whenever they walk. It would be really funny to see serious Order members like Moody or Kingsley trying to figure out how to stop the squeaking while on important missions.
A really funny prank could be where a student's quill is jinxed to write only in limericks. So when they're trying to take notes in class, instead of normal writing, it comes out as comical rhymes. This can be a source of great embarrassment, especially if they don't notice right away. Also, pranks with vanishing ink on important parchments are quite common in fanfiction. The victim thinks they've written important information, but it all disappears, leaving them frustrated and others amused.
One interesting prank could be to magically change the Dark Lord's robes into something ridiculous like a frilly pink dress. It would be a shock to his dignity and his followers' perception of him.
There are some great pranks in fanfiction. For instance, Harry could magically switch the Dursleys' rooms around so that they wake up in the wrong beds. He could also make it so that when the Dursleys try to use their phones, all they hear is a really loud cackling sound instead of the normal dial tone. And another prank could be making the Dursleys' clocks run backwards, which would mess up their daily schedules completely.
One prank could be Harry using magic to make all of Dudley's clothes two sizes too small overnight. Another might be making the Dursleys' living room furniture float whenever they try to sit down. And he could also use magic to make the food on their table turn into slugs when they're about to eat.
In such a fanfiction, Harry might be tortured for information about the Order of the Phoenix. Voldemort could try to turn Harry to the dark side, using threats against his friends.