Shadows of the Damned. While not necessarily underrated by critics, the game was a commercial failure. Underrated by consumers, no doubt. Other games from this generation include Vanquish (commercial failure) and Binary Domain (commercial failure, critical reception was average).
As far as past gen games go, I really enjoyed Jet Force Gemini for the N64. As a Rare game, it never receives its fair due. I also really enjoyed Chaos Legion for the PS2, Devil May Cry's bastard brother. Bujingai: The Forsaken City for the PS2 is a game nobody talks about, but I remember playing the hell out of it. The Bouncer is another PS2 game that I enjoyed but never found a good fanbase. Solid beat-em-up.