Ooo, tough call. Mind you, I've only played through 1 and 3-8. Oh, and Mystic Quest and Legends 1-3, none of which really count.
Cecil is one of my favorite video game characters ever, and a lasting inspiration to me. He almost defines what it means to be a dark knight.
And we can't forget FF1, the classic that started it all.
For story, 6 and 8 are both great, and nearly tied. Both had some great tearjerking moments. But 6 achieved its poignancy without needing to use FMVs and high-tech graphics, so it gets the nod. Plus, 6 has Kefka.
But none of that really matters. This is a game series, so gameplay is what counts. And for gameplay, 5 and 7 are the two I keep coming back to. The major difference is that one of those two features unskippable FMVs in the middle of battles, while the other does not. So the winner is: FF5.