Most of the really good games are part of a franchise but good stand alone games depend on what genre you really like.
For RPGs, Breath of Fire 1 & 2 are good SNES games. They STARTED the franchise there. Illusion of Gaia is another fav of mine. As much as people like Secret of Mana, it is a franchise game, but Secret of Evermore uses the same battle system but is a stand alone title. Chrono Trigger (now is part of the Chrono series) is a fantastic game too.
It's really hard to say others because most of the really good games that had their start on the SNES had sequels whether it be on the same console or elsewhere.