Oh man. I was sort of dreading this year, only because there are so many stone-cold classics. Two of my top 12 games hail from 1994: Super Metroid and Final Fantasy VI.
But my vote has to go to FFVI. Still my pick for best turn-based RPG ever made. Amazing production design, legendary music, pristine combat, and a cast of characters for the ages.
One game I'd like to highlight as an honorable mention: Darius Gaiden. It ranks among the industry's finest horizontal shoot-'em-ups, and it's arguably Taito's magnum opus.