Beyond Good and Evil (Gamecube)
Okami (Wii)
Fire Emblem Path of Radiance (Gamecube)
Snatcher (Mega CD)
Silpheed (Mega CD)
Faxanadu (Nes)
Disaster day of crisis (Wii)

The problem is what we consider hidden gems, low sales or low scores?

Spongebob The Movie Game
Grim Fandango!
Final Fantasy VII =)

too many to count?
God Hand - GoW series will never be as good as that game even if SCE Santa Monica sold their souls to Devil,
Okami,
Cubivore,
Beyond Good & Evil,
Icewind Dale,
Operation Flashpoint - Modern Warfare series is like shovelware compared to this game,
Gun Valkyrie,
P.N. 03,
Cave Story - best castlevania/metroid style game on pc EVER and it's free,
The Longest Journey 1 and 2,
Heart of Darkness,
Stonekeep,
Dewy's Adventure,

all Larry games up to 7,

Grim Fandango,

Hopkins FBI - anyone know this adventure game,

YESSSSSSS!!!!

I want Freedom Fighters 2, damnit!

The games i am going to list are hardly hidden but under-appreciated perhaps (when it comes to sales)

The main one being the fantastic work of art that is Shadow of the Colossus, that game is just WOW!!

The other being a current Gen game, Prince of Persia... I loved the art style of the game, and while Elica can be infuriatingly annoying sometimes, the game is brilliant fun

Iron Soldier 1 and Iron Soldier 2 for the atari jaguar,
first they are 2 of the best games on the console, yeah I know out of all 10 games worth playing on the jaguar doesn't say much but these 2 would be great games on anything
unlike most games on the console both IS games actually had good frame rates,great sound track, technically proficient graphics (IS2 is the best looking jag game, by a lot), great controls, and an actually professional looking presentation
Plus the game gives you a real sense of power when piloting the iron soldier, Tanks, Trees, houses, step on 'em, don't like those skyscrapers toss a grenade and watch them topple, you can literally flatten entire cities if you feel like it.

It's already been mentioned twice, so I'm not sure if it counts, but Folklore is an awesome game that no one bought.

Cave Story (Doukutsu Monogatari)
http://cache.kotaku.com/assets/resources/2006/10/doukutsu.jpg

King's Bounty

Arx Fatalis

I think by Hidden Gems i mean games good games with no sales and that slipped under the radar , i think this generation a lot of Wii games gonna have that status, Deadly Creatures, De Blob, Little Kings Story, House of the Dead, Okami and many more, ahh and one more hidden gem for me would been Castlevania for N64 call me guilty but i liked it.

I agree with Freedom Fighters (GC). It is my favorite squad based shooter to this day. The squad control was just great.

Another hidden gem is The Incredible Hulk: Ultimate Destruction (GC). Don't be fooled by the fact that it is a licensed game. It is the best sandbox game I have ever played.

The Simpsons: Hit & Run (GC) is a lot of fun. It is the best Simpsons game I have played, and I played quite a few of those when I was younger. As the title suggests it's a driving game.

SSX Tricky (GC) is another game that is just a lot of crazy-fun. It's an arcade type snowboarding game.

Star Wars: Clone Wars (GC) is the best Star Wars game I have played. This game is mostly vehicle combat. Sometimes in the air, sometimes on the ground. There are also a few missions you play on foot as a Jedi.

I wasted hours and hours a day on Gauntlet Legends (N64) when I was younger. It's a simple hack and slash, but is very addictive.

Yet another great licensed game is Disney's Aladdin (SNES). It is a really great, fun platformer. A big plus is that this game is a lot of fun to speed run.

As for more recent games:

Excite Truck (Wii) is a crazy-fun racing game.

de Blob (Wii) might be the best 3D platformer other than Mario that I have played.