If you don't count Kain/Cecil/Rosa and Cloud/Aeris/Tifa, then that kindof destroys most of them. The only ones I can think of are Squall/Rinoa/Seifer and Tidus/Yuna/Seymore (Although I'm not sure if that one counts)

Cinna/Cinna's Hammer/Cinna's Garnet Doll gets my vote.