Are there any hidden websites out there? For example a hidden youtube website with only unlisted videos? Or a full blown hidden community? If so how do these websites operate and what are the domain names?
The internet is a giant place. I'm sure somewhere out there theirs hidden websites. There are some right here on tumblr. For example password protected blogs.
Example: http://www.1337lowball.tumblr.com/
I'm not sure how they operate as I don't run one and have no way to interview one. But I would assume they run by family members and very trusted people.
For example I could tell my cousin to join my hidden forum, and he'll tell his cousins and friends and so on.
I personally think these private websites trying to run a community would be nearly impossible to run.
Starting a community is already hard, now imagine starting a private community. It'd probably just be a way for pedophiles to share minor porn online without being spotted. I think that's the only reason why anyone would feel the need to lock there website up.