p9o1p: How to install HD Mod in Quake and Quake II GOG?
Do you mean this HD Mod:
http://www.moddb.com/mods/quake-hd-pack-guide If so then there are instructions in the Zip on how to install it, they are for the original and for Steam, but it should just be a matter of replacing the path names for that with your GOG ones. I assume you browser downloaded the files, ran the main file, and installed Quake to somewhere on your C: yes? If so make sure its out of the windows area, e.g. put it in c:\games. Then (depending on the mod, and I am not familiar with this one) you either extract the zip and overwrite the files in your game install, or copy it to a specific mod directory, again check the instructions.
I may have a look at this when I get home.
Edit: Or maybe it is this HD mod:
http://www.moddb.com/mods/quake-hd-remastered If so, according to the instructions you just drop the files into your install location.