Some obscure and/or underrated RPGs across various systems I have enjoyed that are not Final Fantasy (excepting one I couldn't resist listing) or Dragon Quest. I could literally go on for days, but here are just the first few that came to mind.
NES:
Faxanadu - Sort of an action RPG Zelda II clone with stiffer controls, but this game is fun and kept me going for a while.
Wizardry: Proving Grounds of the Mad Overlord - I suppose this is a fairly well known game, especially among the classic computer enthusiasts here, but I played and loved this brutally old-school dungeon crawler on the NES.
SNES:
EVO: The Search for Eden. This game is probably more platformer than RPG, but the goal is to grind your creature and evolve it into any of innumerable interesting combinations. Fun.
Terranigma - This game rocks. A refinement of the Soul Blazer/Illusion of Gaia action RPG formula, the game boasts amazing visuals, a quirky but sentimental plot, and gameplay that can go toe-to-toe with the better games in the Mana series.
Earthbound - Not an obscure game by any stretch, but too good for me to omit from this list. I never thought I'd own the cartridge given its relatively steep price, but I received it as a gift and loved every second of it.
Genesis:
Pier Solar and the Great Architects: I only heard about this game in December of last year, but I promptly put my name down on the order list for the second production run, and I don't regret a penny of that 40 dollar purchase. You can burn the soundtrack to play in your Sega CD if you have one, but I prefer the PCM. A long, beautiful, 16-bit RPG, fairly traditional in its mechanics, but done very well. Phantasy Star IV is no longer lonely at the top of pile of Genesis RPGs - this game gives it a run for its money.
TurboDuo:
Ys Book I & II - this game has the weirdest combat system in the history of everything (run into the monsters in real-time) but the game has a slick presentation and an engrossing quest. I must caution, however, these games have been ported to a million other consoles, including the DS and PSP, so you might want to invest a more recent edition.
Saturn:
Panzer Dragoon Saga - Yeah right. I can't afford this one. But I hear it's pretty good.
PS1:
King's Field - This game really (and I mean
really) shows its age with ugly visuals, poor framerate, and minimal explanation. It's also supposedly the first fully polygonal first person game on a home console. But this game sucked me in with its staggering challenge, highly interactive environment, and sprawling game world. Give it a shot, but be warned: it was too frustrating for me to play it legitimately on my PS2 with its sparse save points and propensity for sudden death. I eventually got further into it by popping the disc into my computer, running it on ePSXe, and using savestates.
N64:
Quest 64 - I hate Final Fantasy Mystic Quest, but understand why it appeals to some, because the "beginner" RPG Quest 64 appeals to me. Colorful visuals and a fairly straightforward plot and design compliment an interesting magic system. I have a lousy attention span, but this game's charm kept me coming back for more. Just make sure you have one of those damn controller paks to save (and don't cheap out and get the off-brand).
PS2:
Rogue Galaxy - Think Disney's Treasure Planet, but made in Japan and actually
good. This is from Level-5, who also did Dragon Quest VIII, and this is part of their winning streak of stellar RPGs before they stumbled with White Knight Chronicles. I bought this new and didn't regret it.
.hack// - Were you one of those wierdos who enjoyed Phantasy Star Online? Were you one of the even more selective group of wierdos who enjoyed PSO
offline? Try these single-player games out, crafted in the style of MMOs. You even check your email and frequent message boards. Also, there were, like, seven of these games, but they were episodic (a series of 4 games, followed by a series of 3), so start with the first game of either series and see how you like it. Oh, and I still play the Gamecube version of PSO Episode I & 2. The splitscreen is fun.
The Persona Series: Not that obscure, and definitely not underrated, but they are a bit niche and don't carry the same brand recognition as Final Fantasy. Still, with their modern-day setting and unique fusion of dungeon crawling and social simulation, Persona 3 FES and Persona 4 are in my opinion the very best RPGs the PS2 has to offer, and that's nothing to sneeze at, seeing how the argument generally boils down to whether the PS2, PS1, or SNES has the best RPG library of all time.
Gamecube:
The Baten Kaitos Games - Be warned: weird card battling system ahead. Stick with it, and everything starts to make sense. Made by Monolith Soft. Anybody still reading this post knows who they are.
Nintendo DS:
Infinite Space - This is a hard science fiction RPG with an emphasis on bridge-commanded ship-to-ship combat. Not a lot of people on this forum share my enthusiasm for the game, but it struck a chord with me.
Orcs and Elves - a sort of 3D turn based rogue-like from id Software. Short but sweet. Runs on the same engine as the Doom RPG for mobile phones. In fact, while you're at it, grab Doom RPG II on iOS. It's fun.
PSP:
Crisis Core: Final Fantasy VII - Compilation of FFVII was part fan-service, part cash-cow, but this one game in the series really can cut the mustard and stand as a worthy prequel to the original. Mission-based gameplay makes for good portable fun, and the battle system uses an interesting slot machine mechanic. Go ahead and get this one.
PS3:
Nier:
Severely underrated action RPG. The graphics are
so 2005, and the gameplay itself is sort of a derivative hodgepodge of tropes as diverse as Zelda, Bullet Hell Shooters, Resident Evil, and frigging Donkey Kong, but this game has far and above the
strongest story and soundtrack I have ever seen in a Japanese game. May make grown men tear up. I implore you to give this one a try. Also available on 360.
And Speaking of iOS...
Guardian Saga: I'll be honest and tell you I grabbed this game because it went free for a day. Now you'll have to pay like 3 bucks for it, but the game is a very charming homage to the original Dragon Quest and games cut from the same cloth. I couldn't put it down from start to finish, and it took me a good 3 days.