God, scrolling through my AO3 history for this is gonna take a minute because there are so many. A lot of them hinge on taking the sheer weirdness of the 'Naruto' world at face value and just letting the characters bounce off each other. The absolute classic, the one I keep going back to, is 'Team 7's Excellent Adventure'—it’s not the official title but that’s how everyone refers to it. The premise is that a mission goes so catastrophically sideways that Kakashi, Naruto, Sasuke, and Sakura get stranded in some random civilian town with no money and no chakra for a week. The comedy isn’t from slapstick, really; it’s from watching Sasuke, the last Uchiha heir, try to haggle for groceries while Naruto accidentally becomes the town’s unofficial handyman-folk-hero. Kakashi’s deadpan commentary over his stupid Icha Icha book while the world burns around him is peak. It works because it respects the characters’ core personalities but puts them in situations so mundane they’re utterly bewildering.
Another vein of humor I see a lot is what I call the 'found family sitcom' setup, often centered on the Akatsuki of all people. There’s a whole subgenre of fics where they’re forced to share a hideout and it becomes this terrible roommate comedy. Deidara and Sasori bickering over art supplies, Kisame trying to cook for everyone and nearly burning the place down, Itachi just trying to get some quiet to read while Hidan screams prayers in the next room. The funniest ones don’t make them soft, exactly—they’re still dangerous criminals—but the sheer petty annoyance of living together brings out a weird, grumpy domesticity. The humor is dark, dry, and comes from the gap between their terrifying reputations and their incredibly petty daily conflicts.
For a more chaotic, crack-treated-seriously energy, anything that involves time travel or dimension hopping usually has great moments. Like, a fic where a post-war Naruto ends up back in time during the Chunin Exams and just decides to mess with everyone by giving absurdly accurate but useless advice. Watching him casually deconstruct Gaara’s entire tragic backstory to Gaara’s face over a cup of tea, or prank a young Kakashi by knowing all his summoning contracts, creates this hilarious dissonance. The comedy there is in the audience’s foreknowledge and the characters’ utter confusion. I find those fics can get convoluted plot-wise, but the character interactions in the moment-to-moment scenes are pure gold.