1. Final Fantasy VI
  2. Chrono Trigger
  3. Suikoden II
  4. Dragon Quest V
  5. Final Fantasy IX

That sounds like a good list. Though I really consider #1 and #2 to be on the same plane, and #4 and #5 are roughly on the same plane as well. Honourable mentions to Final Fantasy V, Chrono Cross, Earthbound, Secret of Mana, Seiken Densetsu 3, and Super Mario RPG.

I need to play Mother 3 one of these days. Also I just realised how old-school this list is. There is nothing from a system past the PlayStation on this list.