Metroid Prime - I preferred an actual controller the series, especially this game
Wind Waker - one of the best Zeldas
Eternal Darkness - it look/feel dated, but I still love this game (awesome story and gameplay, and I think it controls fine)
Tales of Symphonia - the best game in the series
Skies of Arcadia - a fantastic, old school RPG; give us a

ing sequel already!!
Pikmin - 2 is worth playing, but I honestly liked the original way more
Viewtiful Joe - a great game that doesn't use a unique look/feel to hide mediocre gameplay
Beach Spikers - a great volleyball game (how often do you hear that?) that was overlooked
Mario Sunshine - not the best 3D Mario but it was fun and challenging
There are many more but most have been re-released elsewhere (RE4) in a superior format or aren't that notable on the GC (Resident Evil 2, 3, CVX).