My favorite would have to be Final Fantasy VI by far. Yes, I consider it the absolute pinnacle of the series due to a number of factors.

The Villain.

Kefka was truly a villain and not the standardized "gloomy pretty boy with a grim past." He was beyond all redemption. He was a coward, a thief, a liar and a murderer without any pride, honor or purpose other than wanton destruction and appeasement of self. The moment when he poisoned Doma river had to have been the boiling point. After that, I just utterly despised the clown. No villain since then has ever really made me feel the same way Kefka did. Oh, and the way he killed Leo was just too fucking disgusting.

Celes.

I really can't remember myself ever crying more than I did when Celes decided to jump off that cliff. It was just such a touching moment portraying utter despair and hopelessness perfectly. She's easily one of the most memorable protagonists ever to me.

The Opera Scene.

The most gorgeous scene ever in a video game? I've yet to see anything even come close to this very epic piece.