I'll do my obligatory Xenogears reference, amazing game that many people adored when it came out but just disappeared in the ongoing fangasm of VII fans and the hype of the upcoming VIII. It has a following on the net but the game has never really reached mainstream or critical acclaim (despite getting amazing scores when it was originally released).

I will also go with Jade Cocoon and the Digimon games. I will also add Sly Cooper. Yes the game did very well but it always was the black sheep of the "Sony Trinity". Despite doing amazing gameplay, characters, and story. People were more interested in the "FPS wannabe" of Ratchet and Clank and the "GTA wannabe" of Jax and Daxter.

SMT series also gets a worthy mention. Its nice that Persona finally brought it more into the mainstream and Atlus is willing to bring them out but it seemed like years before it really caught on and the main series is pretty damn snazzy.