I'm actually playing Sword of Mana, the remake on GBA, at the moment. It's a pretty fun game, but not without its share of flaws. But then, nobody played that either, since Legend of Mana sucked and people lost interest in the franchise.

Lemme see... SkyGunner for PS2. It's an arcade-style flight shooter a la Ace Combat, albeit published by Atlus here in the States. Like every other Atlus game, it enjoyed only a small print run, but even many other fans of Atlus-published games have never heard of it.

Actually, I could fill this entire list with Atlus games, so I'll just mention every Shin Megami Tensei game prior to Persona 3. 

Return to Krondor for PC, the sequel to Betrayal at Krondor. Not as good as the original, but pretty decent in its own right.

Astal, a Saturn platformer which I believe was created by Sonic Team. Pretty innovative gameplay, and it's also goddamn beautiful.

I'll say Full Auto 2 Battlelines on the PS3. It was my first next-gen game and I loved it. Sadly I didn't find a lot of people to play online against with that game.

I second Secret of Evermore...

and add...

Chibi-Robo!

One of my all time favourite PS2 games was No One Lives Forever.

I think it was a port of a PC game. It got AAA ratings on the PC, and i think a 62 on PS2.

Story of Thor on the mega drive (Genesis).

Earthbound^^; Seems like everyone I talk to hasn't played that game. It's nonsense. lol :3 Anyhow It's a 2D RPG with tons of humor and a cool HP system :3

Glover, as I remember it, it was an awesome game you could beat with one hand :3

I always forget the name, but it was the 7up game where you played as the dot. I was addicted to that game.

 Here here! Anachronox was one I was going to mention. The game is absolutely hilarious. Arcanum and Bloodlines are also awesome though I think they're a bit more well known.

Thunder Brigade (PC). It's a hovering tanks game, with nice graphics and had a level editor too. unfortunately the campaign had an escort/defend mission :(

Another one is Vangers, but I didn't even play the game that far and I guess even the devs don't know how to play the game or even what the game is about :P

Hybrid Heaven is a good game and I've got the FF Adventure and Secret of Evermore to. Man it's sad that games like that are on this list. I would add Kartia, Custom Robo, Front Mission Series, 7th Saga and Paladins Quest.

The last one has sucky graphics but interesting gameplay. Oh and R-Type Command. That's a pretty good game.