Two interesting ones I've played quite recently, relatively classic but good :
.
Lagrange Point (NES) : This one is a sci-fi JRPG, and a very good one.
Exploration is nice, it's not free but you visit different planets and you have to unlock new suits, vehicles and key items to reach previously unreachable areas, revisiting previous planets from time to time. The third tier of the game is particularly good because you eventually open a big playground with a lot of things to do.
You start with one character, and you have to choose your companions from a big cast of characters to find, many of them are theorically missable I guess, and they all have their own skills.
Encounter rate is high but the classic turn-based combat is fast and it is above average, the total number of different skills isn't impressive but at least you get to use a lot of them ; the characters are different and trying to build the best team is fun and useful.
The game is not very talkative but the story is nice, with a lot of cool situations (and it feels like a 100% sci-fi game, unlike Star Ocean 3 for example). I must say I haven't played some if not most of the usual suspect ones (Xenogears...) yet but I think it's the single best sci-fi JRPG I've played so far.
. Super shell monsters story (SNES) : This one is a very classic fantasy JRPG but it's interesting if only because of the amount of content (locations, quests, characters, skills).
You start with one character and there is a big cast to choose your companions from, a lot of them are available as soon as you reach the adventurer's guild and some more must be found (at least one is secret). Each character has its own class, they're all very different with different stats and they all have a big range unique skills to unlock.
The classic turn-based fights themselves are OK, a few enemies near the end have some very weird skills but overall the game would have benefited from more enemy skill variety.
In addition to the companions which help you in combat, you'll also find other ones which only come with a non-combat skill.
The world is big and filled with a lot of content, exploration is not completely linear, there are some parts in the story with multiple things to do, a lot of side content, in particular each character or so has is own side quest (generally including a dungeon) and you'll have to bring the character with you if you want to unlock the side quest, so if you want to complete every side quest you'll have to use every character at least for a little while. The game is long, and some dungeons are very good with a lot of hidden stuff, in particular the first ones.
The story is nothing to talk about but the locations are varied and the dialogs are often funny, you also get different dialogs depending on the characters you bring with you, not that they are particularly interesting but it's still a cool feature.