Apache overwrites the Lion configurations and I needed to reconfigure Apache to run my localhost websites. Among other the AllowOverride All permissions in /etc/apache2/httpd.conf and /etc/apache2/extra/httpd-vhosts.conf caused my WordPress Permalinks to throw 404 Not Found errors.
If Apache is not running, start the server manually with

sudo apachectl start


Disk Permissions were broken, causing me to be unable to access among other the Applications folder from Finder. I could access the folder from the command line and was able to run the Disk Utility and repair Disk Permissions.

open -a /Applications/Utilities/Disk\ Utility.app/


Reinstall X11 from http://xquartz.macosforge.org/trac/wiki/X112.7.2.

Reinstall Command Line Tools from Xcode > Preferences > Downloads > Components to reinstall gcc.