Banjo Kazooie, and more importantly Banjo Tooie for my son, he had them both on N64 but Tooie got pinched after him only playing one day :-(
I love loads of the suggestions up here, Perfect Dark, Golden Eye and Duck Hunt with wii controls sounds nice :-)
As for Majoras Mask, well I got that for the gamecube so no need for a VC version imo