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.