Like X-Men Apocalypse, Shrak, Malice... any way to get them to run?

Put the mod data in it's own folder in the folder where the exe is. Then, run the game with the "-game folder" parameter.

So for example, if the folder to quake is "D:\GogGames\Quake" then put the xmen quake mod in "D:\GogGames\Quake\xmen"

The existing "Launch Quake" shortcut just runs glquake.exe. Copy that shortcut and change it. Add "-game xmen" as a parameter. You can do that for any mod. Put the whole mod into a folder, then use "-game folder_name" to run quake with that mod.