My favorite games which (I think) not many people have played are:

Pikmin, its got popular now but back when it was released it wasnt that way

Fire emblem, the whole series is really good, yet not many people have played them, i guess since they have releases on the Wii and Gamecube now, they are a bit more known.

Skies of Arcadia, I played this years ago, now I think of it, the game was pretty dark and brutal. Excessive death of enemies created a dark foreboding atmosphere, yet the main character's where never really sad. Oh and the most annoying character gets squished when a building caves in on him.