F-Zero GX- Lots of fun but the difficulty ramps up quick. Very fast, smooth, tight gameplay.
Ikaruga - Another one that kicks my ass but I keep going back to.
Wario ware,inc. Mega Party Games! - I haven't played this version but I played through it on GBA (and the DS sequel) many times, lots of fun.
Mega Man Anniversary Collection - The GC version suffers from a fatal (to me) flaw: The A/B buttons are switched: B is jump and A is shoot. And you can't change it in the game settings. Weaksauce.
Metroid Prime - My favorite game on the GC and the reason I bought one.
Metroid Prime 2: Echoes - Excellent game, but I thought the original Prime was just a bit better.
Metroid Prime 3: Corruption - This is a Wii title, not GC
Super Mario Sunshine - Good fun, but my least favorite of the 3D Mario games.