For example Quake 1 , i would like to use Quakespasm , is there a way I can change the executable to run that instead through GOG Galaxy? Or on any game that has source ports and such?

Head to the Quake directory and edit <i>.info</i> file
you're welcome ; p

Or just name your "Quake.exe" as "Quake.exe.bak". Then rename your Quakespasm executable to "Quake.exe" and throw all the necessary files in the Quake folder.

Thank you both, I found the second suggestion worked better, INFO file didn't work out for me.

Thanks again :D