I'm leaving action and strategy RPGs out, because it's too hard to make the list otherwise.
1.) Final Fantasy VI
2.) Suikoden V
3.) Suikoden II
4.) Chrono Trigger
5.) Lunar the Silver Star
6.) Earthbound
7.) Final Fantasy IV tied with Final Fantasy VII
8.) Dragon Quest V
9.) Phantasy Star IV
10.) Final Fantasy X tied with Final Fantasy IX (If the ending parts of nine's story were as good as the beginning, it would be higher.)
Honorable mentions:
Best Magic System: Treasure of the Rudras, or Rudora No Hihou in Japanese. Magic system where you type in magic words and create spells. Learning new spells involves experimenting with different word combinations, eventually you start to speak the language of magic (and no, it's not screwy latin). Not a bad story either, made around the time as FFV.
Best Combat System of all time: Grandia III (shame about the story...)
Best Music not on the list: Chrono Cross (great game too)
Games I haven't played, or haven't beaten:
Xenogears
Persona 3 and 4
Vagrant Story
The end of Final Fantasy VIII
Ys 1 and 2
