Lots of games mentioned in this thread are not underrated by gamers and reviewers at all. System Shock 2, Shadow of the Colossus, Wind Waker, Deus Ex for example are all considered as classics today, Persona 4 will certainly be called a classic in a few years.
System Shock 2 is considered as one of the most influential games of the past ten years, it's considered to have influenced the FPS genre until today.
That's the problem with threads about underrated games. You'll even find people on this site who would say that Super Mario Galaxy is underrated just because it sold less than Mario Kart Wii.
With that said, all games I bought in the last weeks automatically qualify as underrated because very few people on this site know them and even fewer own them (Goin' Downtown, Drakensang, Ceville, Perry Rhodan, The Book of Unwritten Tales). Next underrated game I'll buy: A Vampyre Story (this one is a bit less underrated as more people have heard of it). 