Also gonna say Final Fantasy 6. There's no other Final Fantasy like it. In the ways the story is told, in the scope of the story, in how much time is covered and in how many characters and villains with different motivations are involved in the drama, and how far that drama plays out, it stands out as pretty unique, I think. It also does a steampunk world in a really cool way that's different from all the other games, and the towns and other locations seem more connected and like a real world than generic vacation town A or generic asian town B. I also love 4. 7 has an incredible bad guy, a palpable horror element, and graphics that changed everything, 9 could have been my new favorite but I hated the ending (but the beginning is the best of all), and 10 was the tightest story they've ever told... I just didn't like Tidus up until the end. The voice actor could have been a lot better. Someday I'd like to try it in Japanese.
Also, I haven't finished 12 yet because it doesn't look so good on my HD TV... kind of hoping I'll eventually be able to play it on my PS3 and do some kind of HD smoothing.
My guess is that not as many people have played the SNES games as the later ones. At least that's what I tell myself, rather than believe so many people could miss all the things that make 4 and 6 so awesome.