In no particular order:
-Tales of Symphonia
-Super Smash Bros. Melee
-Phantasy Star Online
-Mario Kart: Double Dash
-Super Mario Strikers (Only with 4 players)
-TimeSplitters 2 and 3
-Conflict: Desert Storm
To me, the Gamecube will always be the multiplayer-console, as I never owned the console myself, but we used to play it at my friends house all the time, so any game with a proper local multiplayer was always in rotation.
Gladius is another one I've heard good things about but need to try.
It's really good, and sadly often forgotten. It's especially great when played in co-op, with every player controlling their own characters in battle and working together.