Hm. Well, I have especially fond memories of Lufia II for the SNES. It was an respectable RPG in its own right, but went a step further by integrating Zelda-style puzzles. A worthy game for any fan of Zelda and Final Fantasy VI.
The SNES was blessed with many awesome RPGs, and one of those was Super Mario: The Seven Stars. That game game broke the traditional mold of RPGs. For example, you had to time your attack and defense moves if you wanted to increase their effectiveness, you could see enemies and move around them to avoid battles, or to make surprise attacks, and the setting is neither fantasy nor sci-fi, as it is something of its own. This game also lead to later Mario RPGs, some of which are pretty darn good. (The Thousand Year Door, for example.)
As for the PC, the pickings are not as good in my opinion, but like most platforms there is something for everyone. In this case, I found that Planescape Torment is always worth a mention. The combat is tedious, but the game has some of the best storytelling in a Western game, and many roleplaying opportunities. Add the excellent atmosphere and setting, and you have one of the rare 9/10 games that are apt to keep that rating.