I haven't looked into it as heavily as @Harvey and @Maurice have, but all of the papers I saw in Roddenberry's archive at UCLA related to the writer's guide appeared to have been done by Gene.
There were many many revisions, but I'm pretty sure they all had to pass through the Roddenfilter to get approved.
It appears that D.C. Fontana wrote at least part of the season 2 bible revision. In her introduction to Star Trek: The Original Series 365, Fontana talks about sitting down with the actors before season 2 to discuss character backgrounds, including DeForest Kelley coming up with his divorce and his daughter. Fontana writes, "In the show's bible, I named her 'Joanna.'"
The 1966 versions are clearly the work of Roddenberry, building off his 1964 pitch document, handwritten revisions that are clearly Roddenscratch, and memos bearing his name. Dorothy was still Gene's secretary when these first documents were created, and her initials are on many of them, indicating she typed them.
Thanks everyone. I suspected that D.C. Fontana had a hand in fleshing out the 3rd rev, but I haven't been able to track down anything specific. I also wonder if her predecessors as story editor/script consultant might have contributed to the earlier revs?
There's not much evidence of input from Carabatsos or John D.F. Black. Arthur Singer certainly didn't contribute, the last revision predated his arrival by an entire year.
Yep, I'm not much interested in Singer, according to Fontana he didn't even bother to read the writer's guide, much less write one.
On a related note, I recall reading somewhere that the section of The Making of Star Trek that expands on the guides technical info about the ship and its various decks was added (or a copy stapled to) the writers guide for the 3rd season. Can anyone verify this, or is this just hearsay.