I'm setting up a new server this evening. I'm wondering what components administrators regularly put into their skeleton directories? Is it all software/mod specific or are there some general things that can be overlooked by beginners?
I usually leave it as-is. If I want users to have certain files in their home directories, it's generally best to make that decision on a per-user basis, after the account is created.
Exceptions would be for specific-use servers, such as pre-populating the public_html directory for a shared web hosting server, or creating the framework for a chroot jail environment. In general, the default files contain well-thought-out options designed to work effectively in the range of usage cases common for that distribution.