See all Apple Hidden Files
There are 2 kinds of hidden files on OS X.

Files starting with . are normally hidden in Unix (including OS X) or Linux systems, but can easily be shown e.g. by ls -la.

In addition certain files (or directories) are hidden by OS X apps ( ~/Library is one example) and generally files inside bundles (such as .apps) are not normally visible.

It is easy to show hidden files in Finder (by changing settings defaults write com.apple.finder AppleShowAllFiles TRUE). This then applies to all files.

Finder addons such as TotalFinder make changing this easier and Finder alternatives such as QuollEyeTree http://binnie.id.au/QuollEyeTree.html let you toggle this for individual directories and show both kinds of hidden files.