To put it to rest here and now, Majora's Mask = Greatest Zelda of all time.

On topic...

1) Persona 4: Amazing story and character developement. Beautiful artwork.

2) Odin Sphere: Not really an RPG, but everyone who wants to do an end of the world plot should play this. No game I feel has done a better job at setting up the atmosphere to make you actually feel like trout is going wrong.

3) Breath of Fire 2: This game is classic turn based RPG's perfected. Not as good as Chrono Trigger or FF VI mind you, but this is a list for inspiration.

4) Xenosaga Trilogy: While I do enjoy 2, really that's only included to show a game maker how to not smurf up a sequal by not following it's example.

The big thing to take from this would be Episode 3. If you have a game with unique characters, it's goofy as smurf to make them all fully customizable. (FF V did alright with it under it's circumstances, and Devil Survivor handled it amazingly but then you have games like FF VII which made your character differences almost irrelevent outside of Limit Breaks). Episode 3 is a great basis for being able to delevope your characters down multiple paths, all of which make sense to the character.

5.) Devil Survivor 1 + 2: I'm done writing, play them yourselves to find out.