Underrated: STALKER, Sam and Max, ARMA.
Underrated: Tales of Symphonia, Fire Emblem: Radiant Dawn, The Legend of Zelda: the Windwaker
Underrated: Jade Empire, No More Heroes, Sonic Adventure, Sonic Heroes, Sonic Unleashed (how can you hate the day levels?) , Suikoden 1 + 2
All those games should have done better in ratings and sales (except No More Heroes... I can't remember their schores >_>)
The World Ends With You, Psychonauts, the Tales series and the Persona series are all criminally underplayed games, but all of them do very well in the reviews.
And there is a lot of old games which have aged pretty horribly. Crono Trigger, Final Fantasy VI, Castlevania: Sotn and Castlevania IV are good examples
... I need to play Castlevania IV someday
Underrated: the Sly Cooper series