*edit* Whoopsies, I just found that there's a modding sub forum, someone please move this thread there.
My buddy ace mentioned the gb player has really muffled audio on the gamecube. I finally noticed the muffle myself so I cracked open the gb player. Thanks to the wonderful nocash documents he mentions the gba cpu pinout which says that the audio lines are pins 6 and 7:
http://nocash.emubase.de/gbatek.htm
The gb player pcb has these convenient "test points" where you can solder wires to the traces and tap the lines:

Sound was clear but had a whining noise. Ace told me a lpf that worked for him so I tried it. Both audio lines have a series 470 ohm resistor followed by a 0.01 uf cap to ground. I built the filter and the sound came out perfect. I wired a toggle switch to go between original system audio and my bypassed audio:

Here's a video where I'm playing music and switching between the audio sources so you can hear the difference:
This muffle may be caused by lpf on the audio lines of the gamecube audio circuit but I can't find any info on the gc audio circuit. It seems like the gb player converts the analog audio into digital and then in the gamecube it converts it back into analog.