Either Secret of Evermore(SNES), any of the Gex games, Zelda Majora's Mask (probably the best in the series and not that many people have noticed it), and... I can't think of anything else right now.
i agree tehpwner i loved Majora's Mask and most of my friends that play zelda games really think OOT or a link to the past is best when they really didnt even give the game a try (and i love that game XD)
I have Sword of Mana for the Gameboy Advance. That's a really fun little game, most JRPGs are generally unheard of, not under-rated, they get quite devout fans, but most go under the radar. Vagrant Story, older Dragon Quests etc.
The Gothic series is very well known, just not by most contemporary gamers. Google Gothic 3 forums (not gothic forums, that could be disturbing) and you'll probably find a lot of fans and expert RPG players.
