Underrated gems?  I bet I could come up with a bunch of those.

Diddy Kong Racing (N64) - Best kart racer of all time until MKWii came out.  It sold almost 5 million, but that is less than every single Mario Kart game.  MK64 sold double that amount even though DKR was far superior.  As time goes by, people seem to forget about it and Mario Kart overshadows it more and more.  Probably because Rare is now with Microsoft and no longer makes games this good.

The Incredible Hulk: Ultimate Destruction (GC/PS2/Xbox) - The best sandbox game of all time.  Combat is deep and fun.  You are the freaking Hulk for Pete's sake.  What could be better?  Even just moving around the map is a blast, something incredibly boring in most sandbox games.

Star Wars: The Clone Wars (GC/PS2/Xbox) - Star Wars Rogue Leader: Rogue Squadron II gets all the love, and yes, Factor 5 was a fantastic developer.  But you know what?  I had a lot more fun with The Clone Wars.  And it had a some really fun multiplayer modes too.

The Simpsons: Hit & Run (GC/PC/PS2/Xbox) - Mostly a driving game in the vein of Crazy Taxi mixed with GTA.  There are a few on foot missions thrown in too.  The entire city of Springfield is created for you to mess around in.  Tons of Simpsons gags all over the game.  Lots of iconic Simpsons vehicles.  The driving and racing and crashing is just so much fun.

Fluidity (WiiWare) - A puzzle platformer with plenty of exploration thrown in too.  Your goal is to collect all the Rainbow Drops to restore the power of the magical book you play on.  The game looks like a comic book, complete with panels that separate the rooms.  You play as a blob of water, but you also eventually get the ability to turn into a frozen block of ice or a cloud, among other abilities.  I think this is the best game on the WiiWare service.  A must own if you have a Wii.

LostWinds: Winter of the Melodias (WiiWare) - An exploration based platformer that makes great use of the Wii Remote.  You control a small boy with the control stick, and use the IR Pointer to control the wind.  With the wind, you can attack enemies, jump higher or farther, and move boulders around among other things.  A great little game, and you might as well play the first one too.  It is just simply called LostWinds.

Perfect Dark (N64) - Rare's follow up to GoldenEye 007, which uses the same engine.  It sold a lot less than GoldenEye, probably because this was an original IP.  Rare took everything they learned and improved upon it.  The game is chock full of futuristic weapons, most of which have cool secondary functions.  The single player is like GoldenEye, which means that your missions are objective based.  You can't just walk forward and kill everything, like what passes for a single player campaign in most FPS these days.  The multiplayer is vastly expanded in this game.  There are bots, and virtually every option is adjustable.  I still haven't seen a multiplayer that matches the customization ability of this game.  Timespliters 2 comes close.  Not only that, but this game solved the problem of being able to quickly switch to the weapon you want when you are carrying about 15 different guns.  Now games only let you carry two weapons?  Boooooo.  I want moar.

Freedom Fighters (GC/PC/PS2/Xbox) - The best squad based shooter on a console.  You can easily comand your squad with the touch of a button.  And they are smart too.  The multiplayer is a blast since you get to wield your squads against each other.

That's eight there.  How about a few more?  Less description this time.

Golden Sun - Great RPG on the GBA.

NHL Hitz 20-02 - Hockey version of NFL Blitz.  Super fun.

SSX Tricky - Great snowboarding game.  Tons of fun.

Art Style: ORBIENT - Simple but challenging puzzle game with a space theme.

de Blob - Best non-Mario 3D platformer I have played in a long time.

Goldeneye 007 on Wii. Everyone remembers the N64 Goldeneye and rightly so but this title did justice to the name! The campaign was fantastic and blended the retro stages with new technology brilliantly and I still play the multiplayer (both local and online) to this day. Very underrated....

Super Paper Mario deserved the hate. Sorry.

I remember renting doom 64, I didn't like it. The maps were pitch black and you couldn't make out anything. They tried to make things too realistic but lost the charm of the original game. I played both the original games and what I remember liking about it was the skill involved in winning, the secrets hidden in the maps (I used to time attack Doom One over and over just to see how fast I could do it.) Doom 64 was the first time I realized how awful FPS's were on a console compared to a PC.

 It didn't. The story is decent, the characters are very likeable, the music is good, the game is full of sidequests and extra stuff to do, the gameplay is enjoyable.. What was wrong with the game? I am dying to hear.

I actually would have a similar list, and agree with many of these. I'd probably throw Eternal Darkness in there as well.

Regarding Super Paper Mario - I actually did really enjoy this game, loved the platforming style mixed with action/RPG elements, thought the transitioning from 2D to 3D was pretty neat, though I wish you didn't have to use it so much to find everything as it made it a bit repetitive. The thing that REALLY bogged this game down for me was the endless streams of text, most of which was completely uninteresting to read. It was so bad that it managed to drag what could have been one of my favorite games of all time into being merely "good," and that's sort of a tragedy..

Kameo - Ahhh, that last gasp of the GOOD Rare. I remember getting this with my Xbox 360 close to launch and being hypnotized by the vibrant and colorful HD graphics. The game was also a blast to play, if not a bit short. I also ran out and got PDZ shortly thereafter, and enjoyed both games immensely. Little did I know I would never enjoy a Rareware game again after those..

Viewtiful Joe - neat action fighting game that kinda reminded me of Final Fight 2, one of the first SNES games I ever played. Though I'd say this one is more of an excellent rental than a great buy, as it was a bit brief as well and once you beat it I didn't really feeled compelled to go back and play again.

Klonoa 1 + 2 Brilliant 2.5d platform games that weren't afraid to tell a story. Music was superb as-well which was fortunate as you could unlock the soundtrack

Ape Escape 1-3. They were a breath of fresh air in the 3D platform genre at the time.

Well I wouldn't want you to die. The gameplay was not enjoyable for me because they removed the rpg elements from combat. The turn-based battles were by far my favourite part of the previous games.

   It's OK if you didn't like the gameplay... I presonally liked it.. Better than Sticker Star a million times. At least in Super Paper Mario you gain exp from beating monsters and bosses.

I´ve played a lot of games that can be considered underrated, but i think the one that deserves mention from my part is NIER. The story, characters, world and quest are on my top, is a game that  leaves you thinking, that finds a place in your memory, and yet it was received with mixed reviews, and hate for the dated graphics and kinda repetitive combat. However i gave it an opportunity years later of it release and was amazing. Is my opinion though.