Eternal Darkness, Beyond Good and Evil, Psychonauts, and Okami.

Although some of those got great critical reviews, they are underrated by the public.

That's not underrated.  In fact, just about everyone who has played it has loved it.

Half the people in this thread haven't mentioned any underrated games at all, just low selling/slightly obscure ones.  Underrated means a game that has gotten a lot of negative reviews, attention, and what-not that you enjoyed. 

I'll go with Sonic and the Black Knight.  This game has gotten panned by critics and whiny forum posters (who haven't played it) alike.  The fun part is that once you recognize the few game boss battles suck and the early levels suck, you also realize that the rest of the game is excellent.  I couldn't help but thinking as I was going through one of the lava levels "Holy crap, this is exactly what a 3D Sonic game should be" because it was just that great. 

The new Turok, the new Bionic Commando (it flopped... so not many people played this little gem), Secret of Evermore, Mother II, most SHMUPs out there such as Einhander and Radiant Silvergun, etc.

Oh yeah, and Custom Robo Battle Revolution, Custom Robo Battle Revolution... Hmmm, did I say Custom Robo Battle Revolution?

pirates of the caribbean for PC

Bully: Scholarship Edition was completely awesome and didn't get nearly enough credit.

Hmm you make a good point WoW. I tend to lump in games that people haven't played but dismiss as underrated even if they have a good average review. However going along with the theme of your post. The Last Remnant (PC). While I think the 360 game is underrated, the PC version improves upon the game in addition to eliminating the technical glitches that were present in the 360 version. Yet the review scores for the PC version of the game are near indentical to the 360 version.

Gungrave Overdose. Love that game!

It was only a matter of time ^

I also think Wii fit deserves an honorable mention