Many things you install in Mac OS X are installed from package files (whose filename extension is ".pkg"). Each time something is installed from a package file, a "Bill of Materials" file (whose filename extension is ".bom") is stored in the package's receipt file, which is kept in /Library/Receipts/ …
Each of those ".bom" files contains a list of the files installed by that package, and the proper permissions for each file.
When you use Disk Utility to verify or repair disk permissions, it reviews each of the .bom files in /Library/Receipts/ and compares its list to the actual permissions on each file listed. If the permissions differ, Disk Utility reports the difference (and corrects them if you use the Repair feature).