ned's blog
Doom 3 - How to install/update. 
How to install and update Doom 3 - ORDER


Fresh install of Doom 3
-install Doom 3
-patch Doom 3 to v1.3.1

Fresh install of Doom 3 and the Resurrection of Evil (RoE) exspansion pack
-install Doom 3
-install RoE
-patch Doom 3 to v1.3.1


NOTES:
The patch v1.3.1 can be run over ANY version of Doom 3
- latest patch info including windows, mac and linux links - here -
The Resurrection of Evil expansion pack patches Doom 3 to v1.2
- If you install RoE after patching Doom 3 then you must reinstall the patch!




!! Custom content like maps and mods can now be installed. !!




PUNKBUSTER

Before going online after a fresh install I recommend you update Punkbuster. Details - here -

What is PunkBuster? - link -
PunkBuster for Players online manual DOOM 3 Edition - link -