Pikmin 1 & 2 are must owns. Miyamoto does it again!!

Nah, it was the PS2 version, I even checked it myself after posting it

You could be right about the Wii one though, I've heard mostly rumors, and knowing some lazy developers out there...

Most of my suggestions have already been said, here's a few more though:
- Fire Emblem: Path of Radiance
- Tales of Symphonia
- Star Fox Assault
- Wario World
- Super Monkey Ball 2 (1 is pretty good as well)

I liked Psi-Ops: The Mindgate Conspiracy more than Second Sight.

p.n.03 wasn't too bad either

Eternal Darkness: Sanity's Requiem

Skies of Arcadia Legends

Looks like most of the games I would say have already been covered. I will throw out a few games I liked though. I could probably give you more, but these two will have to do.

The Incredible Hulk: Ultimate Destruction - Best sandbox game I have ever played.
Freedom Fighters - Squad based 3rd person shooter with fantastic squad controls.

Man, Psi-Ops.  THAT was an epic game.  I don't know how well it aged but I enjoyed that game on the level of a Metal Gear title at the time.  I don't think it ever got released for the 'Cube, though.  I got it on the PS2.

I wanna name some games but you guys already named the ones I'm thinking of.

Some great (but overlooked) games on the GCN... hrm...

There's already been a lot that's been mentioned, so here's a couple more

Donkey Konga 1/2 (Good rhythm/music fun. Don-key Kon-GA!)
Donkey Kong Jungle Beat (Works surprisingly well with the bongo controllers, and it looks fantastic to boot.)
The Legend of Zelda: Four Swords Adventures (It's a hassle to get everything together, but when you do... there is great fun to be had.)

I have learned from experience that when you ask questions like this, the only answers you will get are big name popular games that people don't think enough people played.

The good games that weren't popular never come up. I'd never list a first party Nintendo game as underrated.

I'll throw the 2 Lost Kingdoms into the mix and both Baten Kaitos games. Maybe some Racing Emotion and Burnout 2 if your down with that. P.N.03 if you've never played of it.

And of course, GUN.