OSX 10.8.2 with the Server.app installed.
Wiki server running.
where do these files live? (so that I can customize the CSS as well as back everything up.)
What databases so I need to backup and what is the best way to do this?
Does this Apple note help? http://support.apple.com/kb/HT5585
The location seems to be (see Chapter 6 of PDF, in 2d link) /Library/Collaboration/
OK, looking specifically for 10.8.x, I find this: /Library/Server/Wiki/FileData from here https://discussions.apple.com/message/20876865#20876865
As it turns out most everything is hosted in Postgres and not that customisable much beyond the functions they already allow.
By looking around in the Server.app package I found some relevant files here:
The wiki server runs as process
Oh and look, here are the files you asked for located: