My personal 3 favourite:

1. Chrono Trigger : I like the battle system and its multiple ending. The only game where I actually played multiple times trying to get the endings. I like the NDS version better than SNES one though.

2. Lufia 2 : A SNES game but its story are great although too long for me . It have unique battle system that have range of magic and you actually need to think whether to buy equipment that give better stats or the one that had more useful skills. Its puzzle are also got range from "thats easy " to " WTF "

3. Tales of the Xillia : The story is like most Tales game cough*saving the world*cough with several plot twist but I like the dual link skills (in this case "arte"). Every character feels different than the other which improve the gameplay albeit all tales games is like that. Also like Tales of Xillia 2.