I'm in the same boat. I just bought mario sunshine and loving it so far. I also ordered metroid 2 (my brother has the first which I'll trade with him for until I beat the first one) and resident evil 4.
I really want Eternal Darkness: Sanity's Requiem and Beyond Good and Evil. If you like zelda, reviews say that Beyond Good and Evil is like a grown up zelda type game. I want it really bad but it's hard to find for cheap, it's fairly rare. And let's not forget LoZ: Wind Waker if you liked zelda, although its very different from TP. I already have that but prolly won't play it very soon. Many loved it, many didn't (mostly cause of it's style and kiddishness).
People suggest Tales of Symphonia if you want an RPG, or Baiten Kaitos. Gonna finish the gamecube games I bought already first though. A newer game that was released in 2006 that looks cool is Chibi Robo, but it also looks kind of kiddish so I'm gonna wait on that one too. As someone mentioned the IGN Top 25 is a good place to look too.
I already have a gamecube controller, my brother doesn't play his much so I took one of his, I'll prolly pick up a wavebird when I start making money again in the summer.
Check out www.hitgaming.com for cheap new gamecube games. Shipping is somewhat expensive but it evens out cause the prices are marked down and I highly prefer new copies to used ones. I'm weird like that.