Permissions are the rules that govern access to files, there are similar settings on files in Windows, permissions dictate who can read, write, or execute a file. Each file has three sets of that information, one for the owner of the file, one for members of the same group as the owner (such as regular users or administrators), and one for the world (everyone else). Unfortunately, these files are often modified by applications, installers, and sometimes cookies, and the changes to the permissions can cause certain applications to stop operating correctly because they can't access critical data. Repairing permissions fixes the known permissions of critical files, ensuring that they can be correctly accessed by the applications that need them.
It is always a good idea to fix them from time to time, usually at the first step in diagnosing any system problems.
TEG