This Apple Knowledge Base article explains the Repair Permissions process in detail, but heres the basic gist:
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 packages receipt file, which is kept in /Library/Receipts/ . If you look in the Receipts folder, for example, you should see all kinds of files that end with .pkg, including some that were created when Mac OS X was installed (for example, BaseSystem.pkg). Dont worry, these files dont take up much disk space and you shouldnt put them in the Trash.
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).
However, just because a files current permissions differ from its original permissions as specified in the corresponding .bom file, does not mean that the current permissions are wrong. The reason this feature exists is that sometimes, the permissions are wrong, causing some sort of problem, and running Repair Permissions solves the problem.