FLAC, you say? I spit on your FLAC. Native formats are the way to go.
.HPS - High-Purity Stream: Native Gamecube PCM Stream (type 1)
.ADX - Native Gamecube PCM Stream (type 2)
.AST - Native Gamecube PCM Stream (type 3)
.ADP - Native Gamecube PCM Stream (type 4)
.DSP - Native Gamecube PCM Stream (type 5)
.CFN - Native Gamecube PCM Stream (type 6)
.MINIUSF - Nintendo 64 song file (contains soundfonts and engine instructions for playback)
.VGM - Sega Genesis song file (contains synth patches and MIDI data)