Spider-Man fanfiction has such an interesting ecosystem on AO3. The dynamics readers latch onto really shift with whatever's current in the movies or shows. Right now, the most popular ship by a huge margin is Peter Parker & Tony Stark, tagged as IronDad. It absolutely dominates the tag counts. It's less a romantic pairing and more a found-family hurt/comfort dynamic that lets writers explore Peter's vulnerability and Tony's reluctant mentorship turning into paternal care. The 'Peter has a secret' or 'Tony finds out' tropes are evergreen there.
A close second, and the top romantic pairing, is Peter Parker/Michelle Jones, or 'MJ' from the MCU. The chemistry Tom Holland and Zendaya brought to the screen translated into tons of post-'No Way Home' fix-its and canon-divergent stories. Readers love the academic rivals-to-lovers vibe, and writers enjoy crafting stories where their intelligence is a shared language. It's a much more grounded, contemporary teen romance compared to some of the other options.
Then you've got the classic comic-book holdover: Peter Parker & Wade Wilson (Deadpool). Spideypool remains massively popular. The appeal is the contrast—Peter's earnest morality against Wade's chaotic, fourth-wall-breaking amorality. The fandom loves the 'grumpy/sunshine' dynamic flipped, where Peter is the exasperated sunshine and Wade is the grumpy disaster. A lot of these stories are explicit and play with darker themes, which might be why they generate such dedicated engagement.
It's worth noting that cross-fandom ships also have significant pull. Peter Parker & Loki, for instance, or Peter Parker & Harley Keener (from 'Iron Man 3'), have dedicated sub-communities. Their popularity spikes around relevant movie releases but maintains a steady baseline. The sheer variety shows how Peter, as a character, is flexible enough to slot into so many different narrative roles—the son, the brilliant peer, the moral compass for a anti-hero.