There's tons of good rpgs out there, and it's quite difficult to make out those I consider the best. I do have my favorites, but I like many of them for different reasons. For some games it was the complex story that intrigued me, others had a rather flat or dull story, but a fun and enjoyable gameplay. Those that come to my mind off the top of my head were:
Chrono Trigger (perfectly balanced all around, with a good story and a good gameplay)
Chrono Chross (pretty much same as above)
Xenogears (BRILLIANT story, but the combat system gets repetitive over time)
Breath of Fire 4 (best story in the Breath of Fire series)
Dragon Quest IV (best story of any NES-RPG, even above FF2)
Dragon Quest V (I really liked the story that spanned multiple generations of the hero's family)
Terranigma (one of the best games for the SNES overall in terms of both story and gameplay. Too bad the game is rather short)
Lufia II (best game in the Lufia series, mainly due to the gameplay)
There were lots of others of course that I also enjoyed, ranging from the Grandia series to Star Ocean and Tales of, but there are still games of some of these series that I haven't played yet (Grandia 3 and Dragon Quest VIII are next on my to-do list).