I think it really depends on the fandom. Because lots of fandoms divide themselves up in different ways. Pairing is the most common, but also other things like specific tropes and when it happens in canon. Like, if I were doing a Star Wars rec list, I'd have one of the categories be "time travel fixit" and a few other tropes that are really common, but for fics that don't fit into those tropes I'd organize them by pairing.