Destiny of an Emperor I/II - NES
Uncharted Waters - NES
Crystalis - NES
Final Fantasy Legend I/II/III - GB
Startropics - NES
7th Saga - SNES
Lagoon - SNES
Secret of the Stars - SNES
Uncharted Waters: New Horizons - SNES
Breath of Fire I/II - SNES
Jade Cocoon - PSX
Suikoden - PSX
Guardians Crusade - PSX

Feel free to add more guys.

Shadow Hearts (PS2) came to mind but not really sure what defines "little known" (most people "know" what Suikoden, Breath of Fire, FF, etc. are even though they might not have played them.)

brave fencer musashi (PS2 game) kinda similar to zelda

http://www.gamefaqs.com/ps/196813-brave-fencer-musashi/faqs


Monster rancher 2 (Ps2 game)

The closest thing i can say this resembles is pokemon, monster training game but still very different from pokemon

This post was edited by PartynJesus on May 2 2014 07:27pm

Legend of Mana - PS1

Just an epic game with awesome story, lots of interesting side quest(lines) and insane soundtracks and much more ^^

Breath of Fire III/IV - PSX

Valkyrie profile

Not really unknown, but due to the price to actually own a copy it's rare.

Skies of Arcadia
FF XII - Again not unknown, but certainly underrated.
Legend of Dragoon

Valk was amazing.
Crystal too

Legend of Dragoon - psx
quest 64 - n64
zoids - psx
jak series - ps2
FF IX - psx
Star ocean 1,2 & 3 - psx & ps2
Fallout 1 & 2 - pc
Grandia 1 & 2 - psx

the list could go on for good rpgs

edit

must plays for GBA

Golden sun 1 & 2
Fire emblem 1 & 2

This post was edited by BLGEN on Jun 7 2014 01:01am

Just got startropics and so far its really good.