1. Breath of Fire III (PS)
2. Chrono Trigger (SNES)
3. The Legend of Dragoon (PS)
Honorable mention: Dark Cloud II (PS2), Breath of Fire IV (PS), Grandia (PS), Suikoden V (PS2 / never got to play the others :/), Wild Arms (PS), Terranigma (SNES), Secret of Mana (SNES), Lufia II (SNES)
The SNES/PS-time was really the best for a JRPG-fan. There's not one JRPG this gen, that impressed me. (so far - I'm having high hopes for FF XIII Versus though.)