Apple Tips: Using Disk Utility
5. Verify or Repair Disk Permissions
Permission settings control which users can view or change various items. OSX automatically sets permissions for disks, folders, and files when they’re installed or created. Subsequently, they can be changed by applications and users.
OSX also keeps a record of files installed by the Mac OS X Installer, Software Update, or an Apple software installer, and the proper permissions for each file.
Disk Utility can verify or repair those permissions, by comparing the actual permissions to those records. It can’t repair permissions for your documents, your home folder, third-party applications, or any other files & folders you may have created, since it doesn’t have any way to know what permissions you want them to have.
To reset the permissions on the files and folders in your home folder, see Resetting Password and/or User Permissions.
Thus, you can verify or repair permissions only on a disk with Mac OS X installed. That’s why the options are grayed-out and unavailable on non-OSX disks.
It’s best to do this using the copy of Disk Utility on the same volume as the OSX volume you’re repairing, so it can access the records of everything OSX has installed on that particular volume. If you start up from your Install disc, or a different OSX volume, the records won’t be complete, and Disk Utility may set some permissions incorrectly. See About Disk Utility's Repair Disk Permissions feature for details.
If you do use a different version, be sure it’s the same major level of OSX (Tiger, Leopard, Snow Leopard, etc.) as the volume you’re repairing.
There’s really no point to running Verify Disk Permissions. If it finds errors, you’ll have to run Repair Disk Permissions anyway, repeating all the comparisons. Just run Repair Disk Permissions.
Start the Disk Utility app 
(in your Applications/Utilities folder), and select your internal HD (probably named Macintosh HD) in the sidebar.
Click the First Aid tab and the Repair Disk Permissions button.
While this is running, some messages may appear, and there will be a progress bar towards the bottom.
If necessary, you can click the Stop Permissions Repair button without causing any harm (but Disk Utility will have to start over the next time).
When done, the last message should be Permissions repair complete.
As long as you see that, the others aren’t really significant.
See this Apple article: Mac OS X: Disk Utility's Repair Disk Permissions messages that you can safely ignore for details.