Everyone says these or most of these at some point.
Super Smash Bros. Melee
Mario Sunshine
Metroid Prime 1 & 2
Wind Waker
Eternal Darkness
Animal Crossing
Pikmin 1 & 2
Resident Evil 4
Soul Calibur 2
Prince of Persia: Sands of Time
F-Zero GX
Twilight Princess
Rogue Squadron 2 & 3
Final Fantasy: Crystal Chronicles
Tales of Symphonia
Killer 7
Naruto: Clash of Ninja
Viewtiful Joe
Some personal favorites of mine, some flaws that prevent them from reaching greatness though.
Pokémon Colloseum/XD: Gale of Darkness
Kirby Air Ride
Double Dash
Wario World
Sonic Adventure 2: Battle
Billy Hatcher and the Giant Egg
Pixel Art can be fun.