Mac OS X hides many files and folders (directories) from the Finder, probably for the security reasons. Typically you don’t need to access these folders and shouldn’t mess with them.
Since I install most of my development related tools (JBoss, Apache Maven, MySQL) in /usr/local directory, sometimes I need to access /usr/local folder from the Finder window (for example, setting up Eclipse environment). This can be easily done by pressing command + shift + G (Go To Folder under Go menu) and then typing /usr/local in the popped-up dialog.
The list of all the hidden files and folders on Mac OS X is available here.