1. Super Mario 64 (a classic game that will never be beat)
2. Starfox Adventures (probably the best in the Starfox series to date)
3. Mario Party 4 (all the MP's, with the exception of 9, 6 and 10, have their place but the 4th has the best minigames and courses)
4. Super Smash Bros Melee (imo the best Smash game to date. Adventure Mode, Classic Mode, Fox's voice, the stages, and the narrator was perfect. A truly enjoyable game (Brawl making a close second, Smash 4 in at 3rd and Smash 64 last)
5. Burnout 3 Revenge (I know its not a Nintendo title , but it still is worth mentioning). A lot of the bands I know today come from that game.
I'm not a hardcore gamer so I only could come up with 5. To date, I think the Gamecube possesses the best catalogue of games on a Nintendo console.