Here's the Doom 3 Script command Reference Help File. Should work in Win XP to Win 8.1.
moddb.com download: http://www.moddb.com/members/thehappyfriar/downloads/doom-3-reference-page (http://www.moddb.com/members/thehappyfriar/downloads/doom-3-reference-page)
Doom 3 BFG Command Line & CVar Reference: http://jansimek.github.io/RBDOOM-3-BFG (http://jansimek.github.io/RBDOOM-3-BFG)
If you have other sites with references (IE wiki's), post in this thread and I'll add them to the sticky.
I wrote a small patch for D3BFG which exports the list of commands and cvars into wikitext: http://jansimek.github.io/RBDOOM-3-BFG
When I get motivated again I will make a better layout for the documentation and set up a bot which rebuilds the list periodically from the current source code.