There are a few others that come to mind... Most of them require you to have a BUNCH of cables and a BUNCH of gameboys though to utilize fully. Anyway, these are all gamecube games:
Zelda: 4 Swords
(I think there was a post recently about this being fairly cheap somewhere. The GBA and cable aren't strictly necessary for 1 player mode, but it's sorta fun. If you want to play with 2+ people, you'll need more gameboys, and cables)
Final Fantasy Crystal Chronicles.
Similar to above.
Pokemon Colosseum/XD.
Eh, whatever. I think you can battle or something in this game. =p
There was also a little something you could do in Animal Crossing too. Harvest Moon as well, if you had the GBA game. Finally, IIRC, there was some Metroid game you could link GCN/GBA. I think that's about everything though... The GBA/GCN link thing never really took off.