Assuming we're talking about translations here, the pool of games that are actually worth playing is a lot smaller than I'd like, but there are a few.
I really can't recommend the Madou Monogatari series
enough (though I may be just a bit biased, as you can see from who released most of these patches). They're mostly dungeon crawlers, but if you're one of those people who reject anything first-person as an RPG on principle, the SNES game
is a conventional overhead RPG. Lunar: Walking School
is a nice Game Gear RPG based on the Lunar series. Royal Stone
is another Game Gear game; it's an SRPG and I haven't played it personally, but it's supposed to be one of the best games on the console.
Games based on popular anime licenses sometimes had enough money put into them to result in a good game: Sailor Moon: Another Story
is well regarded, as is the SNES Magic Knight Rayearth game
(though the translation patch is oooold and I haven't played it personally, so I don't know how it holds up). A lesser-known title is Eien no Filena
, which is actually based on a novel series IIRC. It's not as as good a game, but beggars can't be choosers.
Unfortunately, a lot of older games with female protagonists are "bishoujo games" that are just trying to use sex appeal to entice men into buying mediocre-to-bad games, which I don't much care for. Though if that's what you're looking for, you've certainly got more options...