Does GStudio6 use the same .wad format as Half-Life and Quake? Will Nem's tools work with it? Is there any documentation of the format?

No it´s not the same I think; And a documentation for .wad files I´ve never seen, not in the wiki and either in the manual. You could post in the 'Aks Conitec' forum, i´m sure one of the developers will help you

I know you can add Half-Life and Quake .wads into a 3DGS project and the textures work in the WED editor and engine. If that's any help.

It's when you create a .wad in WED and then try and use it elsewhere, the format isn't recognised as Quake. At least the Wally wad editor doesn't.

Hiya.

The .wad format is different, as it supports 32-bit textures inside the wad. From what I know, you're limited to 256-colors for HL and Quake...I know when I have "Quake" selected as the game when using QuArK to make maps, it will not let me use the "standard.wad" for 3dGS.