For the first 3 Quake games, do the GOG versions contain all the content of the Steam versions?
By "all the content", what exactly are you referring to? Maps, music, skins, expansions, what?
I know that the GOG version has the CD music for Quake 1 and Quake 2 which are missing from the Steam version, and Q1+2 come with all the official expansions. Q1 doesn't have Abyss of Pandemonium, though, which was semi-official, but I don't think the Steam one has that either. It is freely available on the internet though as it was re-released for free download.