I'm trying to think of RPGs that don't break the mold in some way, they just do everything an RPG does really well.

Skies of Arcadia
Final Fantasy 5 (I guess the job system is a little different)
Chrono Trigger
First or second Star Ocean
Final Fantasy 9

Good ones that go outside the mold to some degree

Shadowrun for SNES
Earthbound
Zelda (first one, LttP,)
Secret of Mana
Xenogears
Final Fantasy 6-8
Betrayal at Krondor

That leaves plenty of room for other recommendations.