My favorite is still either Dragon Quest V or Terrangima. Terranigma was a really fun romp with a great storyline, music and characters, along with stellar gameplay, but it didn't hit the correct spot emotionally.
That's where Dragon Quest V succeeded. It's an emotional game. Here you have your innocent little boy, exposed to so many of life's horrors so early on. Yet he is able to recover from these tragedies and go on to become a wonderful husband and father. It was a beautiful game.
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