This is such a hard question.
There are so many good games, especially on the SNES.
With the Chrono Trigger, FF6, Zelda LLTP, Breath of Fire, Secret of Mana...
Rather than talk about those I'll tell you my top 3 games that some people might not have played.
1) Legend of Dragoon
A perfect game (although the art and CGi are kinda dated now).
I especially liked the story and the combat system which was different than other.
It wasn't enough to simply mashed X to beat the enemies.
2) Radiata Stories
My favorite game from Tri-Ace.
The story is awesome with a critical choice in the middle, which leads to two very different story in the end.
With over 175 recrutables characters, every single characters (including NPCs) follow a schedule during the day/night rotation. This feature is still one of the coolest I've seen and his seldom used even in recent games.
3) Breath of Fire 3
The Breath of Fire series holds a special place for me, being the games that brought me to RPGs. And although BOF2 was my first, I have to admit that BOF3 was the best of them all.
For anyone who hasn't given Breath of Fire a shot, consider trying this game. I'm sure you won't regret it.
Radiata Stories might be a bit harder to find (still worth it though), but both Legend of Dragoon and BOF3 are on PSN.
So you have no reason to not play those games!!