I've had a few. Brace for impact:
Radiant Historia:
A very well-done JRPG with a storybook feel and well-realized adult characters pushed along by something of a suspense-thriller story, equipped with an original grid-based battle system. A highly polished and thoughtfully produced stand-out in the genre.
Lost Odyssey:
Same as above, but notable for being an effort from Mistwalker/Sakaguchi to spearhead Xbox interest in Japan. That failed, but we got a real melancholic and classic Final Fantasy in all but name out of it.
Metal Max 2 Reloaded:
A post-post apocalyptic RPG of sorts where you play as a mercenary in a rebuilding world. It's completely open-ended, with mind-boggling customization with character creation and unique recruitables, classes and subclasses, tanks and vehicles with modifiable parts, dozens of quest lines, apartments, wife simping, minigames, gambling, etc.. Features a very smart NG cycle that remixes the location of items and vehicles. I think many here on the Codex would love this one if they gave it an honest effort. Has an excellent fan translation.
Super Robot Wars OG Saga: Endless Frontier and EXCEED:
Pure relentless HOT-BLOODED madness set in the mecha universe that ties the SRW games together. Starts you off with a cowboy hustler trying to catch a mythological mecha on the loose and tame it, like some sort of legendary horse in the wilderness. Overloads you with cute and sassy girls, manly dudes, comic mischief, hilarious banter, KOSMOS from Xenosaga, and pure unrelenting mayhem with a strangely sincere and romantic fantasy retro anime spirit.
Cyber Knight I & II:
These are scifi fantasy JRPGs with mechs and space exploration, with grid-based combat in random encounters, and if that wasn't niche enough, they were made explicitly for "experienced role-playing gamers only" according to the director. They will bust your balls and crush your spirit. The dungeon designs are gauntlets similar to Phantasy Star II, but with significantly harder encounters and painful resource management, and bosses that require air-tight rotations to beat. However, you get to meet God at the end of the first game, who is at the center of the universe, and the sequel directly continues from that experience. And no, you don't fight him. You actually make friends with him and he encourages and praises you for making it through everything.
Tenshi no Uta/Song of the Angel:
This one looks a little basic on the surface, but it's unique for being a love story told on the Super Nintendo. It actually has a decent one, helped by a remarkably competent fan translation, with good characters, and is overall wholesome. It's a fight between angels and demons, and has you going into hell to confront Satan himself to rescue your wife. It's a very traditional fantasy with very little WEEB and DESU, a very Codex grognard-compatible classic JRPG if there ever was one. It almost feels like a western game. Has great portraits, character designs, and fantastic pixel art for the enemies.
Lennus II:
This is technically the sequel to Paladin's Quest on the SNES, but it can be viewed as its own separate thing. It has a lot of similar mechanics and an equally weird and fascinating art style, with surrealist science fantasy worldbuilding and unique races. You can definitely see the Mobius influence here. This one in particular is notable for having what is probably the best-realized city in any JRPG of the 90s, competing with anything in the genre itself. It's an enormous horizontally sprawling complex, with multiple districts, slums, etc.. You have everything you can think of here, and not everyone is friendly or beneficial either. You can eat at an exorbiantly overpriced restaurant and go into debt and have to take out trash to pay it off, forge a green card to get around the city, recruit morally dubious magicians. It's incredible stuff. Has an exceptional fan translation too.
These are the ones that come to mind first. I've played a lot of other enjoyable ones too, but they were probably too weebslop or samey to mention here.
