If I had to pick one game, I'd go with Shadowrun on the Super Nintendo. I've said in other posts that it's my favorite SNES RPG, and it's the truth! That game gets overlooked pretty often, since there's so many other 16-bit RPG's with critical acclaim, but for my money, it's just as good as any Final Fantasy or Phantasy Star game. Look it up!!
Edit: Upon looking at prices, egad, this game has skyrocketed! It's not exactly affordable, but if you can get it on the cheap, look into it!
One game that *is* cheap, and often overlooked, is Hybrid Heaven on the Nintendo 64. It's a pretty cool sci-fi RPG, with fighting game elements. Definitely one of my favorite N64 games, and pretty unique, too!