Secret of Mana as all-time favorite, first reason being Flammie, second reason being the peaceful atmosphere of walking through lush areas with the best RPG music I've ever heard, third reason being able to see enemies and be capable of dodging their attacks by knowing their attack patterns (so kind of like a real-time battle system that worked).
EarthBound as second favorite because it was just so weird, standing out on its own, and being what I thought was my first "real" RPG. And the Crested Booka is the best enemy of all time.
Super Mario RPG's in third because, as great as it was, it was just too easy and pales in comparison to other RPGs I've played. Super Mario RPG introduced me to the RPG scene, and no other game would have been able to do that for me, but once I got into RPGs, I found others that I grew to like better. However, I'll always remember Jonathan Jones and Croco and Boshi and Bowser-ally.
Chrono Trigger I played through recently and I'd rank it at... well, second, bumping out EarthBound (I lost hope for that game when I had to spend hours leveling up). I turned away from CT at first because of the battle system requiring the allies to wait until their bars filled up before attacking again, but once I got over that it was all smooth sailing. CT is long and satisfying and Frog is the best ally ever. And yet, strangely, I can't name any specific moments that stand out for me in CT... I just know that I enjoyed it a lot. Now, if maybe Mario characters were in CT then I'd enjoy it more.
Why I continue to try to save the world, I shall never know.