It's going to depend on what you're looking for really. My list would include:
Metroid Prime 1 & 2- The first one is preferred, but the second is better than a lot of people give it credit for.
Pikmin 1 & 2- The second one is probably my favorite GC game, though you can't go wrong with either one.
Skies of Arcadia Legends, Tales of Symphonia, Paper Mario: The Thousand Year Door, Baten Kaitos: Eternal Wings and the Lost Ocean, & Baten Kaitos Origins- if you like RPGs, all 5 of these are worth it.
Legend of Zelda: The Wind Waker- This is a great game, that unfortunately has some flaws that keep it from being the greatest Zelda ever. Even so, it's near the top of the list.
Obviously, Mario Kart, Smash Bros., & Mario Sunshine are all good, but probably worth holding off in favor of the Wii sequals. Unless you're a big fan of all these series(like I am), but if you were I guess you'd probably already have had a GC. Also, get Resident Evil 4, but get the Wii version for the better controls. Otherwise, just about every other game mentioned in this thread would be worth it as well.