1. Crono Trigger
2. Secret of Mana
I don't think any game can compete with Crono Trigger. FF3(US) and Crono Trigger would be a toss up for the prize of Best RPG ever made... at least that I played. How can you beat the multiple time eras, the cast of well developed characters, the live action/turn based combat with multiple character attacks, the plethora of story options and endings. God, what an awesome game.
Crono Cross was cool, but just seemed to be missing something.
Secret of Mana was a breakthrough game then ended up fathering a revolution that didn't exist. Real time combat, multiplayer support, memorable storyline... It makes me wonder why games never really capitalized on this style until now (aka FF cyrstal cronicals).
--Waylan