A Few documents are available in various places online -- the teleplays to a few episodes, a couple of memos, the original pitch, a few story outlines -- but I haven't been able to find a hell of a lot. The great treasure troves are in archival collections: the Gene Roddenberry, Bob Justman, and Harve Bennett papers at UCLA; the DeForest Kelley papers at the Academy Library; the Nick Meyer papers at the University of Iowa. You have to make an appointment to see these, but they are all available to the public.
I have transcribed or scanned between two and three hundred documents from these collections, and occasionally remember a bit pertinent to the conversation here. I have been thinking about starting a website or blog to share some of this stuff, actually, but I am hesitant because of copyright issues. (Not to mention that it would be hard work!)