Chrono Trigger
Final Fantasy IV
Final Fantasy V
Final Fantasy VI
Dragon Quest V
Terranigma
Lufia 2: Rise of the Sinistrals
Secret of Mana
Seiken Denetsu 3
Front Mission
Front Mission 2
Earthbound
Bahamut Lagoon
Tactics Ogre
Ogre Battle: March of the Black Queen
Super Mario RPG: Legend of the Seven Stars
Radical Dreamers (technically from a SNES periphial)
Shin Megami Tensei II
Rudra no Hihou
Romancing Saga series
Live A Live

To be honest, it might be easier to list the games that weren't great on this system.

As for personal favorites Chrono Trigger, FFVI, DQV, Lufia 2, and Secret of Mana.