1) Prime 1
2) The Wind Waker
3) Fire Emblem: Path of Radiance
4) Paper Mario: TTYD
5) SSBM
6) Prime 2
7) TimeSplitters: Future Perfect
8) Double Dash
9) Baten Kaitos
10) Soul Calibur 2
idk, those are definitely my 10 favourite GameCube games, not so sure on the order past Paper Mario, though.
EDIT: Dammit, I forgot about Rogue Squadron 1/2 as well.