Azure Dreams (PSX) ; hard as hell, I found, but it definitely was worth a try. Very cool
Chocobo Dungeon (PSX) ; wicked cool dungeon crawler, featuring our friend, Chocobo!
Chocobo Dungeon 2 (PSX) ; same deals.
Chocobo Racing (PSX) ; it was a racing game, not RPG--though did have a RPG-esque story, still-- damn worth mentioning. It has the worst graphics you could possibly ask for--- but it's THE most addictive game I've ever played (and still do on occassion)
Skies of Arcadia (Dreamcast) ; not TERRIBLY rare, but some haven't heard of it-- The plot is as generic and cliche as possible, the battle system is slightly original, and the ship battles are gorgeously fun. I dunno... somehow it's one of my favourite RPGs ever.
the Final Fantasy Legend series (Game Boy) ;
I think they were part of the Mana series in Japan, and translated to the FFLegend series in north america(EDIT: <thanks to Ocean's Dream> it was translated into "Final Fantasy Legend" from the Japanese "SaGa" series), nonetheless, one cool series (3 games, that I know of). You had a team of generic joes and janes, and depending on the game you could pick your race/class/whathaveyou, then throughout the game, eat monster meat (or metal junk) and change into different monsters etc to aquire new abilities. It was a really cool series. I enjoyed them.
The Quest of Dude (PC) 
; it's made by some Dudesoft guy, no one knows much about it.
ARGH (PSX) ; Frig, I can't think of the name right now, but there was a game I bought for the anime cutscenes (I was into anime in highschool, sue me) and the cool battle system shown off in a Playstation Mag demo disc. It had ugly no-faced characters that were years behind technology then, and you had this magical armlet that would transform you into wearing armour and weapons. It was more of an action-RPG, come to think of it.
Omikron: the Nomad Soul (Dreamcast) ; this sort of follows RPG standards... though more towards Shenmue. The battlesystem, that rarely reared it's head (except when you weren't expecting it, and thusly die) was a fighting game style, too. I dunno. Music by David Bowie (he even had an in-game cameo as a singer in a band), bleak distopia city setting (like Blade Runner), good graphics (for the time), pre-GTA free-roaming, and a cool story where you could die, and then wander into the next available person and assume their life.
Jade Cocoon: Story of Tamamayu (PSX) ; Absolute MUST-HAVE. It's a monster-trainer/breeder game... really one of the most fun I had on PSone. You play some kid from a village in the middle of giant monster forest, and trap monsters in silk (?), then use the monster to breed with your monsters so you get a stronger beast... or potentially a super hidden beast... until you beat the game, at which point you unlock a super dungeon crawler level, that sprawls endlessly with challenging bosses at each stage end.
Jade Cocoon 2 was... a similar concept, except they killed it by making the hero a younger punk kid, who was doing monster hunting as a job; and it was at this point in time common place to do, so the whole thing stank of Pokemon. (not that there's anything wrong with Pokemons. :P)
What else... Well, I can think of several very interesting other genre games, but I guess that doesn't apply here. So :P
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