I think because it had such a powerful storyline.
You had the death of Aerith, probably the biggest part to that subject... how many other fantasy games do you know - usually with a "living happily ever after" type ending to them - where you get to know a character, get to have her in your team etc, heck you've even worked hard on levelling them up... and then have them permanently die half way through the game.
Also how you 'led' Cloud from being "Mr. I-don't-care" to a fairly caring person who couldn't help making friends after all, and then you go through a time when you're worried that he was 'constructed', then you lose him, then finally you get the 'real' Cloud. And all the amazing twisty-turny storyline elements that made it so thought provoking, even after the end (or given the abrupt ending at the time, *especially* after the end). I never did 100% understand every element of the story, especially Jenova/Sephiroth and combinations and locations thereof.
Of course, you can't help but admire the story of a group of terrorist underdogs saving the world either
Or the fact that had it not been for Cloud's personal problems, the big disaster they were fighting against at the end wouldn't have happened in the first place....