Really?
There is a couple of things they don't cover, this is the way I normally do it.
1. Run the game. Go to the system, options, and controls and set it all up how you'd like it. Obviously the resolution doesn't matter.
2. Quit and go to the Doom 3/base directory. Open DoomConfig.cfg in Notepad. Find the three lines you need to edit (to set the width, length, and aspect ratio). Make sure you set all three using the directions given on WSGF.
3. Save the file and then set it to READ ONLY. I found that if I didn't do this, Doom 3 would just revert to 640x480 or somesuch when I ran it.
4. Play Doom 3. Note the menus, PDA, and cutscenes will still be in some odd 4:3 resolution. Once you get into the game though, you should have it in your chosen WS resolution.