I'm only putting on one list (Genesis) because that is the only system that I have played a decent amount of RPG's on.
1) Phantasy Star IV - see Lightning Flik's description. It's a almost-perfect blowoff to the series.
2) Shining Force II - I've played this an insane amount of times (due to the Sega Channel and later, emulation), even though I don't own the actual cartridge. It beats the shit outta SF1.
3) Beyond Oasis - A nice Zelda-like game that was also very underrated.
4) Phantasy Star II - It's not higher because of the horribly tedious dungeons. That's the major turnoff of PSII.
5) Shining in the Darkness - A nice RPG that was pretty good for its time. Decent graphics (including 3D mazes), and a decent amount of difficulty make this a winner.
6) Shining Force - the one game that put tactic-style RPG's on the map. SFII was more memorable, though.
7) Landstalker - Another RPG in the vein of Zelda, with a lot more puzzles than your average game.
8) Light Crusader - see 7...plus pushing cows are funny!
9) Phantasy Star III - I'm kinda stretching this, but it did have some redeeming features including the idea of multiple generations and magic redistribution tables.
...I am stretching this.