I posted a forum topic last week like this. Got some great answers/ for me it's The Witcher. One of my all time favorite games.

Beyond Good & Evil is a good game!

Roadrunner's Death Valley Rally. I loved that game when I was younger.

I'd have to agree with Born4This on Metroid being underrated.  Metroid is as classic as Mario but really gets no where as much love even though it plays closely to some of the more modern  Castlevanias. Metroid is good ish.

If I were to pick out an underrated game personally...it would be Sonic CD. Sonic CD was released primarily on the Sega CD and PC. It later found its way onto one of the obscure sonic collection disks. Not even the one that had Sonic The Hedgehog 1-3 but the one that had Sonic the Fighters and the Game Gear ones and Sonic Pinball. Like, really?

The fact that it appeared on the Sega CD more than likely heavily contributed to the fact that it never really was popular or even known. Sonic CD follows the tale of Sonic stopping Robotnik from taking control of 7 gems that hold the key to the passage of time (basically Chaos Emeralds that control time). It plays like most Sonic games for the most part in that it is a 2d, fast paced platformer of the old school.  What makes it so cool is that it was the first and perhaps only Sonic with a hand drawn intro( http://www.youtube.com/watch?v=JPC8W672mXc ) and "cutscenes".  The music in these hand drawn animations just seemed befitting of Sonic to me at the time and cause me to tingle with nostalgia. In addition to this we are first introduced to Amy Rose. Amy is the pink hedgehog who has a love affair with Sonic in the more recent titles. This was her first outing and she is kidnapped by Robotniks latest creation, a robotic version of Sonic. Unlike that pansy from Sonic the Hedgehog 2, the Robotik Sonik in Sonic CD was just maliciously cool and served as a viable rival for Sonic throughout the length of the game, rather than an arbitrary boss. The game even has a boss scenario where you and Robotik Sonik race through a level (like the races in Sonic 3 VS mode) with debris in your way. the Chaos Emerald Bonus stages were 3D-ish in the same manner as those in Sonic 3 (although no where near as grid like). The final icing on the cake was that since this game is based on time gems Sonic can actually rip through the fabric of time.

By going past a sign post labeled either Past, or Future  and maintaining ones speed Sonic is propelled to the Past or Future of that particular Zone/Act. The stage will either be covered in vegetation or over ran by Robotniks goons. In some cases I do believe it was merely cosmetic but was cool nonetheless.  Everything of the game just reeked of cool even to the small details like Sonics newly added Roadrunner-esque speed dash which spooled his feet up prior to bolting off. You'd get hurt running into something since you were not rolling but it was ultimatly reeked of utter coolness.

Sonic CD is definitely a game that slipped through the masses and should be experienced if you liked the old 2d Sonic games.

Uno

We Love Golf.

Best golfing game of the current generation.

I think it's Dark Sector. Underrated AND overlooked. It's actually really fun and I picked it up for $2.99.

Armada on Dreamcast is a definite!  Mixing rpg elements with a space shooter was a perfect combo in my opinion.  I probably logged hundreds and hundreds of hours into that game.  Alot of the Dreamcast games where underated, as was the Dreamcast.  What about E.G.G.? I bet no one remembers that game.  

I would have to say Farcry: Vengence for the Wii.  The AI sucks and it is a little glitchy, but it is really beautiful.  Using the nunchuck and the remote pulling two triggers for two handed gun combat awesome.

The original Red Faction.  The only decent game in the series go figure.

My bet is set on the Legacy of Kain series.  Any game with a solid, deep story is always good in my book.  Top of my list!  A good runner up in the Lunar Series starting way back on Sega CD.  The remakes on Ps1 were great and now a well deserved remake for the PsP.