Mac OS X incorporates a subsystem based on a UNIX-style operating system. In this kind of system, every file and folder on your hard disk has an associated set of permissions which determines who can read, write to, or execute it.
Many things you install in Mac OS X are installed from package files (.pkg ). Each time something is installed from a package, a file (.bom) is stored in a folder of the System or in a receipt file (.pkg). Each of those .bom files contains a list of the files installed by that package, and the correct permissions for every file.
When you use OnyX to verify and repair disk permissions, it reviews every .bom file and compares its list to the actual permissions of each listed file. If the permissions differ, OnyX corrects the difference. If you remove receipts or .bom files from /Library/Receipts/, the files installed by the packages can neither be verified nor repaired. This is why you should not delete things from /Library/Receipts/.
OnyX repairs the permissions of these files but will not repair the permissions of the documents in your home folder.