My pick would be Shadow Madness, made by Grave in 1999 for the Playstation. It has quite an interesting world, lore, and characters that deviate so much from prototypical, generically pretty, glittery JRPG style characters (One's a farmer robot, another is a guy you never see without his steam-punk suit, and another is a floating head). I've played many RPGs, mostly JRPG's, and they're good too, but Shadow Madness I find is just as good as some of the best. The major flaw is the aesthetics of the character models, they're very polygonal and blocky, but much of the scenery is fine and nice. For those who think never-ending walls of text is the mark of an "intelligent" game, you'd love Shadow Madness, because they have lots to say and there are many side books to read to look into the lore on a deeper level, but, unlike a game like FFXIII, it's not totally necessary to read every little thing to get the big picture.
The combat is the only way I've ever seen menu-style, turn-based done at its best. The moment you choose an action, they immediately do it, the turns go by quick, meaning if you act fast enough, you can get plenty of hits in before the enemy, and you can avoid attacks by choosing "Evade" which just moves the character away from the malefactor.
I love Shadow Madness, it has good combat, good characters, good story, soundtrack, and everything else... except pretty character models.

Is Star Ocean: The Second Story a game that flew under the radar?  I'd never heard of it until I happened across it at a used game store.  It was for the Playstation, which was a pretty popular console for its time.  What about Elemental Gimmick Gear, E.G.G for the Dreamcast?  That was a great action-style RPG that may or may not be well-known.   

I think that the Dragon Quest series is pretty underrated... in the west, I mean.

Phantasy Star IV, if you're into old-school games.

I wanna try out the Shin Megami games.

Suikoden III
Soul Nomad
Odium (aka Gorky 17)
Might & Magic (NES)
Ogre Battle

Okage, Dark Cloud, and Baulder's Gate: Dark Alliance

Jade Empire.

Evil Islands

Threads of Fate
Brave Fencer Musashi
Final Fantasy: Mystic Quest
Rogue Galaxy

Come at me.

~Digital Devil Saga 1 & 2
~Ar Tonelico series
~Xenosaga Ep 2
~Enchanted Arms
~Front Mission
~Valkyria Chronicles

o_o Shin Megami Tensei: Nocturne is actually my favorite game, it's probably the only rpg I've played 3 times... I even have some fanart of it, but they look like crap because I drew them ages ago XDDDDD
But well, some RPGs that I thought were great and are not very well-known are Mana Khemia, Shadow Hearts (GREAT series, I highly recommend it), SMT: Digital Devil Saga, and Resonance of Fate, my favorite Xbox 360 game...because well...xbox doesn't have many interesting games anyway o_õ

The World Ends With You

The Bards Tale series (Not that PS2/Xbox game.)
I mean, the original Bards Tale Series, and it's offshoot Dragon Wars. It really stood in the shadow of the D&D Gold Box Adventures.

do you make this thread every 2 months or something