Hmm... well, overall, it would either be FF6 or Chrono Trigger. But both of those fall under the Square umbrella. So what about the others?
Enix: Dragon Quest 4. They had a lot of great others, though, like the quirky Robotrek, and, IIRC, the original Ogre Battle.
S-E: FF6A easily. The CT remake was screwed up.
S-E (no remakes): This is tougher... DQ8?
-dunno001
-On a quest for the truly perfect game; I don't think it exists...