The question isn't which ships are technically "best," but which ones still have a living, breathing fandom producing readable work years later. That narrows it down considerably. For me, the Alex/Stevie dynamic is the foundation. The series built them up, tore them apart, and left them in a weird magical-family-limbo. Fanfiction that picks up from that unresolved tension, exploring their adult lives balancing wizard politics and a human-magical relationship, often has a maturity the show couldn't touch.
Justin/Harper never got the spotlight, but it makes sense. Stories with them are usually quieter, character studies on two overachievers navigating a fundamentally lopsided power dynamic—one has literal magic, the other has... a encyclopedic knowledge of school bylaws. When done right, they're surprisingly thoughtful. You get these low-stakes, coffee-shop AU fics that are weirdly comforting.
Anything beyond the canon pairings is a ghost town now, which is a shame. I remember a brief surge of Max/Rosie fics that played with the mortal-immortal Romeo & Juliet thing, but most of those writers have moved on. These days, the ship tags are pretty sparse, so finding a well-written multi-chapter for any pairing feels like a minor miracle.