I know that people will disagree, but it's definitely Squall and Rinoa for me. I have always loved them as a couple, but I have realised that they are the only ones I truly care about in a serious way, in that I care that they get together and get emotional watching them, whereas the other couples/potential couples that I like in Final Fantasy games simply have a few cute moments to me. I actually watched the "Eyes on Me" scene on YouTube twice in the same night very recently (as well as the ending), and each time I was reduced to tears, the same as I was back in the day. They just always seemed the most believable to me, and the most real to me.

I know not everyone will agree, but this is how I feel about them.