My favorite pairings are:

Aeris/Cloud
Tifa/Vincent
Yuffie/Reno

But, I have to say, my true favorite couple, the one on the top of my list, is Tifa/Aeris. There are several reasons I like the coupling, and I really don't feel like posting them all up here, or at least I don't feel like writing them down at the moment ten minutes before I have to leave for work.