Vagrant Story. VAGRANT STORY. A MILLION TIMES VAGRANT STORY. It may be the greatest game ever made, honestly.
I'll also throw you some curve balls:
Koudelka
Vandal Hearts
Brigandine
Parasite Eve (Very well known, but one of my favorites. I want to get a copy of the novel it's based on at some point.)
If you like your RPGs obscure and in Japanese, check out Ore no Shikabane wo Koeteyuke! It's freaking awesome and it was a real shame that we never got it over here.
I feel compelled to say that I'll sell you my copy of Alundra for cheap if you want it. I absolutely hated it when I finally played through it earlier this year. The story isn't bad, but the platforming is incredibly obnoxious because of the perspective. It plays like a Zelda that focuses more on puzzles over combat, which seems like it would be good, except it totally kills the pacing of the storyline because the dungeons end up feeling like a chore. Most of the solutions are obvious enough, but the jumping can mean falling back to a lower level and having to re-do huge sections. If you're a completionist, you'll find yourself very frustrated at how often certain items become inaccessible after progressing; and if you don't get absolutely everything, you can't get the best weapon in the game. I had to replay the entire first half of the thing because of that.
Blah. "Eye of the beholder," and all that... You may love it. In which case: all the more reason for you to have it instead of me. I have a digital copy on PSN if I ever feel like punishing myself again.