I'll post some I'm sure most people have never heard about - actually most of these are more akin to western RPGs rather than FF-like uberlinear shit due to their nonlinearity and freedom of choice - those labelled (J) are jap only:
* (J)
Weltorv Estleia - it'd be better if I understood what the fuck is written on the screen. Anyway, you can buy houses, complete quests in multiple ways, become a pirate lord and a shitload of other things.
* (J)
Lunatic Dawn II - you create a character, then you're dropped into the world with no directions whatsoever and you can do whatever the hell you want - get married, buy a house and hire more people, start destroying monsters in one area so the towns there will flourish and so on
* (J)
Moon Remix RPG Adventure - this one can't be explained, it has to be played to be believed
* (J - script translated)
Growlanser - it's got more choices and consequences in the first twenty minutes than most RPGs in the whole game (ok maybe I'm exaggerating, but still I was truly impressed by the amount of choices and nonlinearity). 2 is very good as well but not as much as the first one, 3 is decent and 4 onwards they're shit.
*
Star Ocean 2 - well this is more widely known. I like it because it's open ended
* (J)
Taikou Risshiden V - the true game in which every choice has a consequence.
* (J - translation in progress)
Chaos Seed - Dungeon Keeper-like with quests and multiple ways to complete each one. Arguably one of the best SNES games which unfortunately didn't get a translation.
* (J)
Traverse: Stairlight and Prairie - an open ended SNES rpg, you gotta love that
*
Terranigma - again, this came out in the US so it's more widely known.
*
Romancing Saga: Minstrel Song (actually, the whole RS series is great, but I had to choose one so...) - best PS2 game I've ever played
BONUS: (J)
Oriental Blue - read
this and keep waiting for the translation. Hey it's gonna come out eventually.