My first pick would be Eternal Darkness for GameCube, but I'm not sure if that was underrated or not. I just know it was very cool. I really wish there had of been a sequel made to that, because it had a very cool concept that I felt could have been delved into a bit more.
Beyond Good and Evil comes to mind as well. I really enjoyed that game and I don't know how good it did or if there is going to be a sequel.
Does anyone out there have a really strong contender for most underrated game of all time? From the 8-bit gen to the current one, take your pick. I'm pretty sure there will be many valid suggestions.