With the introduction of OS X 10.11 El Capitan the Disk Utility.app no longer offers the option to "Repair Disk Permissions".
With the introduction of System Integrity Protection (SIP), in theory this is no longer necessary.
In previous version of OS X you could use the Terminal.app to "Repair Permissions" with the following command:
sudo diskutil repairPermissions /
With OS X 10.11 El Capitan the command has changed. Use the Terminal.app to "Verify Permissions" with the following command:
sudo /usr/libexec/repair_packages --verify --standard-pkgs /
With OS X 10.11 El Capitan the command has changed. Use the Terminal.app to "Repair Permissions" with the following command:
sudo /usr/libexec/repair_packages --repair --standard-pkgs /