Oh god you done got me started...
My personal faves:
[SNES] Terranigma - I've been on this somewhat obscure game's bandwagon since last year. SNES typical topdown action-rpg. Awesome story involving rebirth and whatnot. One of the best soundtracks for any game ever, pretty good for a 16-bit game.
[SNES] Illusion of Gaia - Gets a ration of crap for being a Zelda imitator, but it was a pretty good game in its own right. Action rpg, cool storyline, not as frustrating as your typical random battle rpg.
[SNES] Earthbound - Off the wall in many ways. Typical console, turn based, topdown rpg. One of the more humorous games you will ever play, but when it decides to get serious MAN does it do it well. Holy crap.
[SNES] Secret of Mana - The crown jewel of all action rpgs. Enjoyable epic story. Amazing soundtrack.
[SNES] Secret of Evermore - Alot like SoM except it involves a wise-cracking American kid, his dog, and TIME TRAVEL. A load of fun.
[PS1] Dragon Warrior VII - Turnbased, topdown rpg. This game is 100+ hours of straight storyline mode alone. There are about 32 different "worlds", more like vignettes, before it all really converges together on the second disc. Plays like an oldschool NES rpg, even though it has 3D environments.
[PS1] Final Fantasy IX - If you only play one Final Fantasy, play this one. You really feel the fantasy, epic feel to the story. The character development is fantastic, including the villains. The soundtrack is of course absolutely incredible.
[PS1] Final Fantasy VII - This game really is very very good. Has a more modern feel to it than many other RPGs, excellent character development, and an excellent story especially if the twists havnt been revealed to you yet by the internet
[PS1] Final Fantasy Tactics - Turnbased strategy, much different from usual rpgs. The best story of any RPG I've ever played. Character development out the ass. Incredible musick.
[N64] Ogre Battle 64 - Another good strategy-ish rpg-ish kinda game. Another incredible storyline, involves some things you might like (demons, bouts with insanity, etc).
[PS1] Parasite Eve - Relatively short, but intense horror-action rpg.
All I can think of right now.