Final Fantasy VI (III US).
After playing FF VIII, I started playing VI on my SNES emulator. I wasn't expecting such a deep, long and complex game. No rendered FMVs, no 3d anywhere, just some pixels that are supposed to be the characters.
Still, it might be the best Final Fantasy EVER. At least on par with VII imho.
The character design/development is awesome and there are so many characters.
And the best, I thought I was fighting the final boss, and I (somewhat) lost the battle, the world ends and I noticed that I just completed the first half of the game. Wow!
Same applies to Chrono Trigger (which I'll buy again for my DS in a few days).
Time travel rocks!
It's kinda sad there are almost no games today, that have an equally deep storyline.