Not sure about each module, I think you'd need some basics that're always public. Especially stuff that's discoverable through other means, illusion of privacy is bad.

But yes, definitely want to have non-public website. My site is currently my LJ, but at some point I want to close down my LJ for search engines so that everything comes here, a reverse link is bad for that, but I'd still like users here to know how to find me there if they prefer reading there.