vincent/yuffie is both pair the spares and "opposites attract" with bubbly cute energetic ninja4broody scary emo vampire

rufus/tseng is popular because of the boss/subordinate master/guard-dog thing they have going on and also they're both attractive

hojo/vincent is popular with a niche subset of noncon medfet whump fans

these are definitely popular among people who want M/F with rude or reno, there is a fanbase for these and you often see reno/elena as a background pair in M/F fics:
reno/tifa
rude/reno
reno/elena

this pairing has a small but VERY devoted following based on how tseng was so creepy fixated on aerith:
tseng/aerith

this is not popular at all despite having some people into it enough to write fanfiction over the years but it should be way more popular imo:
rufus/reeves

biggs/wedge has been popular over the years as a kind of joke background ship but idk how it is now with remake

kadaj/kadaj/loz+sephiroth was really big when advent children was newer and the brocon incest enthusiasts went wild but idk what that side of fandom's like now