Legend of Legaia 2: Duel Saga was a pretty neat RPG. I liked it better than the original because I could actually beat the damn thing (some of the bosses in the original were ridiculous). The skill/battle system was great, it had a lot of puzzles and sidequests (always a favourite of mine) and while the story wasn't anything too mind-blowing, it was decent for what it was.
Legend of Dragoon gets a lot of love from me, too.
One that I haven't seen mentioned yet - and maybe it's not considered underrated, but I've not met many who've played it - was Okami. God, that game<3. From the art-style to the battle mechanics and story, it's very much worth playing.
Breath of Fire series, especially the second. A lot of people that have played them usually prefer the third or fourth over the second, but personally it's my favourite of the lot. Also, on the SNES games, Secret of the Stars, the original Star Ocean, Secret of Evermore and Illusion of Gaia/Time are all great titles.
Lufia II is usually overlooked by people who have played it due to them preferring the original, but I think it's the better game of the series, with charming characters, lots of great tunes, interesting puzzles all over the place and that awesome 100-floor randomly-generated dungeon. Also, three New Game + modes~<3
Terranigma is an amazing game and a lot of people have never heard of it or played it. It's really worth experiencing at least once. The gameplay mechanics are very smooth (I recommend playing with a controller if you're gonna go emulate it), the characters are entertaining and the whole game is wonderfully polished. Also, there are some awesome tunes in there~<3
http://www.youtube.com/watch?v=8_dUWSH_86Q
One that wasn't released in English, but now has a fan-translation, is Ein no Filena. The battle system is different, the setting and story are great, the characters interesting and the graphics very nice. The only main issue with it is that the music is a liiiiiiittle repetitive. But it's well-worth checking out if only to play as a cross-dressing, possibly-lesbian female hero in a gladiatorial setting. Have I caught your interest yet?
This is where I'd throw in a line about Suikoden II and how it's usually considered the lesser of the two first titles in the series but instead I'm going to jump to another game that is often considered pretty awful when compared to the game that came before it. Yes, Chrono Cross. I know, I know. It's not the best game out there, but it has a lot of charm, replay value out the wazoo and the music... oh God, that heavenly music. It's worth playing at least once if only to know how the Chrono story 'ends'. And to hear that music.
Lastly, a little game I loved to death if only for the Introduction movie music - Wild ARMs. The original one, with the princess. Not many people I talk games with actually ever heard of it which is a damn shame, because the story, characters, battle system and music is pretty great. It's got a Western theme happening, but how many games let you find items via radar? Or control a gigantic golem? Also, some of the music is amazing.