Baten Kaitos Eternal Wings and the Lost Ocean is pretty much one of the best RPGs ever made in my book. Tales of Symphonia is a good one too. Of course the Resident Evil games, including the ports as RE2 has its best version on the 'cube. RE3's version is the second best, with only the (albeit heavily modded) PC version eaking out above it.
I also enjoyed my time with titles like Sunshine, Luigi's Mansion and Pikmin, though they aren't as great for me anymore they were still good fun. Eternal Darkness is fine, with some really unique twists that will stay with you forever but the overal gameplay was mediocre.
Special mention should go to the easily forgotten Rogue Leader. People tend to overlook it since it was a (semi?) launch title and was overshadowed by things like Smash Melee (duh) but it's absolutely without a doubt the best use of the IP I've seen and an absolute PASSION project. Insane game.
Then there's the eternal classics. Metroid Prime is absolutely one of the best games ever produced in terms of complete package on all fronts and its sequel is no slouch either. Wind Waker is a timeless beauty too.
It's also home to Twin Snakes, a remake that's overly hated (though understandably) but still fantastic. F-Zero GX is the best racer ever produced imo while Soul Calibur II definitely has the best version on the 'cube due to Link. Paper Mario is great too, but I admit to only having played it through once since it's so long.
Lastly I want to talk a bit about Path of Radiance which imo is the absolute pinnacle of the fire-emblem series. It has the best plot, versatile and mixed up maps, great bonus-objectives, fantastic camp-mechanics, supports, optional stuff, heroes, soundtrack, pricetag hahaha. Just a timeless gem and one I often find myself replaying.