Hi,
I've download Space Quest 1,2,3 and am happy to have a great download and 'cloud storage' of my old games (kinda) through GOG :-)

That said, if I play SQ3 through DosBox SVN Daum with MT-32 ROMS setup I get perfect MT32 audio.

The games downloaded from GOG seem to be hard coded for Dosbox and FM Audio from SoundBlaster - can I download any game that supports the MT32 from GOG and modify the settings to use the MT32? I saw an article regarding SQ1,2 here but it didn't address the overall issue of FM Sound being default - maybe the MT32 code isn't included with GOG releases?

1. The games aren't hard coded to use SoundBlaster, the Setup programs are just missing. You can easily switch the devices by opening RESOURCE.CFG and replacing SNDBLAST.DRV with MT32.DRV where applicable.
2. You may want to use ScummVM for all games that are supported by it as ScummVM includes the MT32 emulator and allows to set up audio devices more conveniently. You just have to place the ROMs in the the main folder of each game that you want to use it and then choose the corresponding audio devices from the GUI.

Edit: Also according to this list SQ1 and 2 do not support the MT-32, only the 1991 remake of SQ1 does.

On top of what F4llout said, a third option that I personally use is to install Munt (+BASSMIDI) because then you get universal MT-32 support for all your DOS games, no matter whether they are GOG games, games you have separately installed into DOSBox etc. Then you can run the GOG games directly with MT-32 music (as long as you set them up to use MT-32 with the sound setup, like F4llout instructed), without having to use them either with your special DOSBox build, or using ScummVM with those games that support it. So it is harder to set up the first time, but after that I feel it gives more freedom to get MT-32 support in different releases.

And yeah as said, Space Quest 1-2 don't have MT-32 support, in fact I think they don't have any PC sound card support, so what you are hearing with them is actually PC beeper sounds. Space Quest 3 and Space Quest 1 VGA remake certainly have sound card (incl. MT-32) support. I think the first Sierra game that had MT-32/Adlib support was probably King's Quest 4 (1988), anything before that didn't, at least in the Quest games.