Unsanity.org: Exercises in Futility Part 2: Repairing Permissions is Useless
"Repair permissions" is a common recommendation for OS X troubleshooting. Personally, I've had permissions problems with applications (incorrect group), but OS X disk utility repair permissions did nothing (I fixed the problem manually). This article explains why; the OS X utility seems only to repair permissions on a some core systems files. Any other permission problem, typically due to bad behavior by an app installer, cannot be fixed this way.
In practice corrupt preference files and corrupt caches are a much more common problem source than permissions repair.
The more savvy the tech writer, the more likely they are to say repairing permissions is grossly overrated.